Some workers contracted by the MTA to help with the homeless scourge at transit hubs spent more than half their time in the office — often with the door shut and a “Closed” sign telling vagrants seeking support to come back later — a damning new report shows.

Auditors with state Comptroller Tom DiNapoli’s office observed the troubling behavior on both announced and unannounced visits over four years involving Bowery Residents’ Committee workers at Grand Central Terminal and Penn Station, the report says.

The company has a $2 million annual contract with the transit agency, according to the DiNapoli audit.

BRC staffers observed by the comptroller’s office 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.

“The MTA is not getting what it paid for, and riders and the homeless are suffering for it,” DiNapoli said in a statement.

The $2 million MTA contract covers Penn Station, Grand Central Terminal and the Long Island Rail Road and Metro-North stations inside city limits. DiNapoli’s auditors found the BRC short-changing the MTA at all of the locations.

At Penn Station, DiNapoli’s auditors caught outreach workers ignoring homeless individuals knocking on the outreach office door to seek services.

At Grand Central, service workers spent just 14 percent of their time conducting outreach, the report said.

Auditors also found inconsistencies and falsehoods in BRC’s reporting practices that raised red flags about whether proper outreach was being conducted at stations, DiNapoli’s office said.

The city’s homeless crisis has been a scourge on transit service, with a 50 percent spike in homeless-related snafus through the first three months of the year compared to 2018. The vast majority of those incidents caused service delays.

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