It follows SNP members on South Ayrshire Council leading a successful move to rip out a segregated cycle lane in Ayr.
SNP councillors also helped to scrap an extension of the Bears Way segregated route between Milngavie and Glasgow planned by East Dunbartonshire Council.
A cycle lane in Perth city centre has also been removed to make way for parking.
Mr Yousaf said he was “disappointed” by such moves and said the new working group would seek to remove hurdles hampering the development of more segregated lanes on roads.
The Scottish Government sees these as crucial to help to meet their “vision” of 10 per cent of journeys being made by bike by 2020, compared to less than 2 per cent just now.
This is because segregated lanes are viewed as more likely to encourage inexperienced and timid cyclists than lines down the side of roads.
Mr Yousaf, who was attending a cycle summit in Stirling to day, said: “As this Scottish Government is investing record amounts, I want to be certain that public money is invested wisely and that barriers to more effective delivery are understood and overcome.
"Too often bold visions get bogged down in the delivery.
"Recently, I have been disappointed with some decisions taken locally about cycling infrastructure which will hinder the achievement of our long term vision – in particular the installation of segregated cycle lanes on the streets of our towns and cities.
"That is why I am establishing this task force to look at how we can tackle the practical barriers to delivery of ambitious cycling and walking projects in Scotland.
“I am determined to make this task force work through local democracy and in doing so ensure better community consultation, better communication and ultimately better active travel [walking and cycling] infrastructure that is good for local economies and communities.
“It is only by working together we will be able to deliver a 21st century cycling infrastructure that befits our ambitions for healthier, more prosperous communities who are less reliant on the car as a mode of transport.”
The task force will be chaired by the Scottish Government's Transport Scotland agency and start work following the publication of the updated Cycling Action Plan for Scotland next month.
A draft version of the blueprint recommended focusing on increasing cycling in cities and large urban areas because the 10 per cent “vision” was “unlikely to be achieved” by 2020 as it was unprecedented globally, Scotland on Sunday revealed in July.
There was no mention of the goal in information issued with the minister's comments, but Mr Yousaf has previously said he is determined to stick to it.
News of the task force came as Mr Yousaf launched new funding contest for segregated routes following Â£3.25 million being awarded to the Â£6.5m South City Way scheme between Glasgow city centre and Queen’s Park in August, in a previous round of the initiative.
The two-mile route is due to open in summer 2018.
Mr Yousaf said such schemes could be a "game changer" for boosting cycling.
The latest round of the the Community Links PLUS competition is seeking "ambitious design projects, restoring balance in Scotland’s streets in favour of people walking and cycling".
Initial entries must be in by next month, with up to Â£50,000 development funding available to entrants, with the winner announced next summer.
Keith Irving, chief executive of the Scottish Government-funded co-ordinating body Cycling Scotland tweeted last week: "Holmston Road dedicated cycle lane in Ayr removed this week at huge cost and against professional advice & all policy. Very disappointing."
The task force was applauded by cycle path developers Sustrans Scotland, which runs the contest.
Acting director Daisy Narayanan said: “We welcome the announcement of the working group and look forward to hearing further details.”
"The vision and ambition of the South City Way from Glasgow City Council is testament to what can be achieved in partnership, and we look forward to working with local authorities and other key stakeholders to encourage similar innovation elsewhere across Scotland.”
Sustrans Scotland national director John Lauder said of the latest round of the competition: "We’re seeking big, bold projects that not only enable more walking and cycling but boost local economies, make streets safer, more attractive places, and create healthier communities."