After the mayor announced punitive new policies that would order families who don’t work tossed out of city shelters and their children put in foster care, a coalition of city’s shelter operators did a rare thing: They took a stand. Now, the city’s Department of Homeless Services is literally making them pay for their audacity.

In December, the Tier II Coalition, which includes 42 of the groups that operate the city’s homeless shelters, encouraged its members to refuse the mayor’s new policies. Nearly all of them joined the boycott, and the majority skipped a special training session that DHS had organized to teach them the new rules. Tier II shelters provide emergency housing for about 3,600 families every year, billing the city for the service.

Now, at least a half-dozen of them are wondering what happened to their checks. Normally, DHS pays shelter operators each month for the families they housed the month before. But in January, many shelters instead got notice that their checks were stopped, with instructions to call DHS Commissioner Martin Oesterreich’s office for a knuckle-rapping.

“Basically, they were reprimanded for having taken a position in opposition to the city, were re-read the rules in terms of compliance with contracts, attending meetings, and toeing the line,” said Gloria Nussbaum, executive director of the Tier II Coalition. “It was a little routine that folks had to go through.”

Shelter operators report that after their visit to the commissioner’s office, their checks appeared to be freed up and are now going through the normal administrative check-cutting process. “[Oesterreich] did release our money,” said one shelter operator, who asked not to be identified for fear of retribution. “I think he just wanted people to call up and grovel.” DHS did not return repeated calls for comment.

“It’s kind of the big stick approach,” agreed Nussbaum. “That the administration has used the contracting process to seek revenge against critics is not new; that’s why HUD has taken away the city’s control of federal homeless funding,” pointed out Legal Aid’s homeless policy expert Steve Banks. “It’s clearly an attempt to chill criticism of a completely misguided shelter plan.”

Mayor Giuliani threatened back in December to shut down any shelters that disobeyed his new rules. The regulations, however, are still hung up in the courts and have yet to take effect.