The MTA is launching a task force dedicated to combating the growing homeless crisis in the city’s subways, the agency announced Wednesday.

The task force, expected to be created in the coming days, will design a plan centered on “housing alternatives and increased resources” in an effort to significantly reduce the number of vagrants and panhandlers swarming the transit system, the MTA said.

The team — which will include reps from the NYPD Transit Bureau, MTA Police and the state Office of Temporary and Disability Assistance, alongside MTA managing director Veronique Hakim and chief safety officer Pat Warren — will have 30 days to create the plan.

It will look at issues including better ways to measure the number of homeless people on the transit system, “enhanced enforcement” of subway rules, as well as the possibility of establishing a “dedicated homeless outreach office within the MTA,” the agency said.

The number of vagrants sleeping in the subway system has spiked by 23 percent this year, according to the city Department of Homeless service’s annual head count.

The announcement comes after Gov. Andrew Cuomo sent a letter to the MTA board earlier this month demanding the homeless issue be addressed as part of an agency reorganization plan.

It also comes just a day after a damning audit released by state Comptroller Thomas DiNapoli found that workers contracted by the MTA to help with the scourge at Grand Central Terminal and Penn Station were often holed up in their office while ignoring vagrants at the transit hubs.

A subsequent probe by the MTA’s inspector general found similar slack behavior by the contractor, the Bowery Residents’ Committee — with IG Carolyn Pokorny saying she personally witnessed people rooting through garbage cans for food and sleeping right in front of the BRC office at Penn Station.

The probes focused on contracts the MTA has with BRC to work at the two transit hubs and commuter rail stations, but the city and MTA also have a separate $9 million contract with the outfit to patrol the subways, which will be the next target of DiNapoli’s auditors.

On Wednesday, a City Hall spokesman said the city would continue to work with the BRC despite the disturbing findings.

“We take the Comptroller’s findings very seriously and we are investigating this matter,” said Avery Cohen. “BRC is a crucial partner in our homeless outreach efforts and we’ll continue to work with them to ensure they are meeting the needs of our most vulnerable New Yorkers.”

MTA chairman Pat Foye called the findings “appalling.”

“We pay [BRC] a lot of money. They’re a well-regarded organization, I’m told,” Foye said after the MTA board’s Wednesday meeting.

“But not answering when the homeless knock, and not coming out and having conversations with… is appalling and unacceptable.”