The MTA’s inspector general has launched a full-scale investigation into a homeless-outreach non-profit contracted by the agency — after a pair of inquiries found workers holing up in their offices instead of offering their services to vagrants, according to a letter obtained by The Post.

Auditors with state Comptroller Tom DiNapoli’s office observed the behavior on visits to offices of the Bowery Residents’ Committee at Grand Central Terminal and Penn Station over four years, a report from his office says.

They found workers from BRC spent just 26 percent of their time conducting in-person outreach to homeless individuals — half the 47 percent to 59 percent required by the firm’s contract.

In a separate inquiry, MTA Inspector General Carolyn Pokorny and her staff observed similar incidents over six days of site visits culminating on Tuesday, including at least 20 occasions when homeless individuals were unable to access BRC services because no one answered the door or staff turned them away.

“BRC appears to be providing, at best, minimal outreach services–often turning away those seeking assistance and, at worst, completely ignoring homeless persons seeking assistance,” Pokorny wrote in a letter MTA Chairman Pat Foye obtained by the Post.

“I personally spent several hours inspecting Penn Station and saw individuals seeking food in garbage cans just steps from BRC’s Office door and homeless individuals lying on the ground directly outside BRC’s Office,” she said.

The city and MTA have a $9 million contract with the group to patrol the subways.

City officials and a BRC spokesperson declined to comment. Transit officials told the Post the agency is taking steps to hold BRC to the terms of its contract.

“The MTA is taking aggressive action to address the troubling performance issues on the part of our contractor brought to light by this report,” MTA Communications Director Tim Minton said in a statement.

“The MTA will tighten oversight of the BRC’s outreach workers, and will hold them accountable for results.”

Additional reporting by Ben Feuerherd