Grant Shapps has found "unused" bike lanes clogging traffic and has accused some town halls of misusing specialty funds for "green" transportation.
The transport minister said he was "unwilling to tolerate poorly designed road closures" that resulted in traffic being "secured".
He also unleashed his anger on new bike paths that "profound changes" are imposing on entire communities.
Last month, pictures taken across the country showed bike lanes that were empty or nearly empty as traffic passed on narrow streets.
Research by MailOnline in London, where Transport for London runs its own £ 33 million program, showed that on Park Lane in Mayfair, only 21 cyclists were using the bike path when 400 cars passed.
Mr Shapps' comments in a letter sent to local councils last week come despite the fact that many of the bike paths were built with money from a £ 250m emergency fund he revealed in May.
Grant Shapps has found "unused" bike lanes clogging traffic and has accused some town halls of misusing specialty funds for "green" transportation
The program should encourage walking and cycling after the coronavirus lockdown.
The town halls were asked to apply for the money by developing projects to lure people away from their cars.
The Sunday Telegraph reported yesterday how critics complained that some of the money was being spent on poorly designed road closures and new bike lanes that increased traffic.
There were also protests that disability groups, local residents and businesses were not being consulted because the systems were put in place under the Covid emergency powers.
The main roads that were struggling to recover from the closure were also affected as the number of visitors was reduced.
In the letter sent on Friday, Mr Shapps appeared to admit the problems and accused a "remarkable number of councilors" of "misusing their funding".
He added, "I've seen or heard … of far too many instances where temporary bike lanes, because of their location and design, were not used while their creation supported traffic alongside them."
Explaining how he has since ordered staff to work with local councils, the Minister of Transport added: "Since then, numerous systems have been scaled back and revised."

Last month, pictures taken across the country showed bike lanes that were empty or nearly empty as traffic passed on narrow streets. Pictured: an almost empty bike path on Park Lane in central London

Motorists expressed their anger at the delay in their journeys when they stood next to the free bike lanes. Pictured: A pop-up bike lane in Sale, Manchester

Pop-up bike lanes, set up as part of the £ 250million plan to get Britain moving again, are empty as traffic squeezes onto narrowed streets and brings the capital to a halt. Pictured: A pop-up cycle path on West Derby Road in Liverpool
He warned that in the second round of funding, some town halls could get "considerably less" if they didn't adopt a good design.
His letter came after MailOnline's investigation of the UK's almost empty bike lanes last month.
On Euston Road in central London, only seven cyclists used the designated lane during a 15-minute period in which 400 cars drove by.
In Liverpool, on the busy West Derby Road arterial road, only two cyclists used a pop-up bike lane for 15 minutes during rush hour, compared to 300 cars.
Motorists expressed their anger at the delay in their journeys when they stood next to the free bike lanes, while cyclists complained that idling made air pollution worse.
Research also showed that congestion rates in London were higher in September than they were before the UK lockdown in March.
The new bike lanes are part of Transport for London's government-funded Street Space program, which aims to encourage people to walk or bike to work and school as an alternative to public transport after the lockdown is eased.

MailOnline visited some of the main bike lanes during peak rush hour to see how busy they are and found that they were chronically underused as they criticized cyclists and motorists. Pictured: a pop bike lane in Tooting High Street, London


Our research shows that on Euston Road (picture) in September only 7 cyclists used the designated lane for a period of 15 minutes, while 420 cars fought through traffic

Similarly, the pop-up bike path on West Derby Road in Liverpool was seen empty as cars lined up in traffic from bumper to bumper
In Manchester, where a similar program was in place, a popup lane lasted only 48 hours before being removed by the council after outrage from drivers.
In the capital, the busy Euston Road – one of the main arteries running through central London – was reduced to a single lane to accommodate the bicycle lane, resulting in a halt.
Richie Clea, who drives around London repairing gas pipelines and is stuck in traffic along Euston Road, told MailOnline in September: “Driving in London is getting worse. There are too many bike paths that nobody uses.
“My travel times have tripled since the lockdown ended. It's a nightmare. & # 39;
Cyclist Graham Robinson added: “The bike lanes have not been properly thought through. It has led to more traffic congestion and the air quality is deteriorating. It is quite common to ride a bike and be hit by a large cloud of smoke or bus smoke. Cycling in London is not for the faint of heart. & # 39;
George Peach, who cycles nearly 12 miles to his advertising job every day, said, “The roads need to be improved, not narrowed. The traffic fumes are getting worse and worse and where there are no bike lanes you fight for space against drivers. This program is supposed to make us healthy, but I worry that you could do more harm because there is more pollution. & # 39;
400 cars were counted over a 15-minute period on Park Lane, another main street in London, compared to just 22 cyclists.
The builder Norman Adams said the cycle lanes introduced by Transport for London had "ruined" London.
He raged: & # 39; What's the point? The Mayor of London, Sadiq Khan, keeps talking about air quality, but how does that stack up when cars sit idle with engines for ages? He just hates drivers and wants them to pay. & # 39;
What is believed to be one of the main bike path junctions at the intersection of York Way and Goods Way near Kings Cross Station, 40 bikes were counted in 15 minutes, but overshadowed by 360 cars and vans passing by time.
Things didn't go much better further out of central London as traffic piled up next to empty bike lanes and some cyclists chose not to use them at all.
In Hammersmith, west London, MailOnline counted 18 cyclists, more than half of whom did not even use the lane and opted for the road, while two others loaded the pavement. At the same time, 280 cars were crowding around a busy main street.
Shortly after rush hour in Ealing, West London, 45 cars were counted passing in fifteen minutes, but only three cyclists using the designated lane and one on the road.
Ironically, the local council was one of the biggest beneficiaries of Street Space funding, recently receiving nearly £ 440,000 for providing cyclists.
The only place that bucked the trend was Tooting in south London, where 100 bikes were counted on the bike path.
Unfortunately, the number of cars passing could not be calculated as they were all stuck in a terrible traffic jam.
Across the country, councils have begun raising funds from a total of £ 250 million to spend on cycling to keep people fit and to get out of their cars as part of the war on coronavirus.
The result, however, is that not only drivers have suffered in London.
A pop-up bike lane was scrapped in Greater Manchester within 48 hours of the major riot of motorists over long queues.

A pop-up bike path on Tooting High Street was also seen empty as traffic crawled past

Similar programs are running across the country including Liverpool where there is a pop-up cycle path on West Derby Road (pictured)

The road is a major arterial road to and from the city center and is always busy, especially at rush hour

In London, the new bike lanes (pictured here on Park Lane) are part of Transport for London's government-funded Street Space program, which aims to encourage people to walk or cycle after easing as an alternative to public transport going to work and school curfew

The builder Norman Adams said the cycle lanes introduced by Transport for London (pictured: Park Lane) had "ruined London".

What is believed to be one of the major bike lane junctions at the junction of York Way and Goods Way near Kings Cross Station counted 40 bikes in 15 minutes, but dwarfed by 360 cars and vans passing by time. Pictured: A new pop-up bike lane on Park Lane

Across the country, councils have begun raising funds from a total of £ 250 million to spend on cycling to get people fit and out of their cars as part of the war on coronavirus. Pictured: A new cycle lane on the A56, Sale, Manchester

A pop-up cycle lane was scrapped in Greater Manchester within 48 hours of the major riot of motorists over long queues
The lane was removed by Trafford Council on the A56 between Sale and Altrincham in June after drivers complained about standing in a queue for an hour just to go two miles. Bollards had been put down to give cyclists a trace of the road.
Councilor at the time Nathan Evans said: “We certainly need safe bike lanes, but at a time when we need maximum opportunities for access to work and limited use of public transport by simply cutting the main route into Manchester in half, without proper consideration or Consulting local residents with them is the wrong decision. & # 39;
In London, a Tfl spokesperson previously defended the Street Space program to offer a healthy alternative to using public transport.
& # 39; We urgently need to rethink the use of road space to provide safe and engaging spaces for walking and cycling as an alternative to car use in the context of reduced capacity on the public transport network.
"Suppressing motorized traffic while allowing essential journeys is key to ensuring that we manage our road and public transport networks in a way that allows us to get people moving in the best possible way."
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