After the mayor announced punitive new policies that would toss families who don’t work out of city shelters and place their children in foster care, a coalition of the 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 to implement the mayor’s new policies. (Tier II shelters provide emergency housing for about 3,600 families every year, billing the city for the service.) 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.

By February, at least a half-dozen of them were wondering what happened to their checks. Normally, DHS pays shelter operators each month for the families they housed the month before. But 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 and were re-read the rules in terms of compliance with contracts, attending meetings, and toeing the line,” says 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 they visited the commissioner’s office, their checks appeared to be freed up and were going through the normal administrative check-cutting process. “[Oesterreich] did release our money,” says 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.

“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,” points out Legal Aid 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, hung up in court, have not yet been put in place.