Even as the city is telling hundreds of homeless families that they are not eligible for temporary shelter, scores of rooms in apartment-style nonprofit shelters are sitting empty, according to a coalition of organizations that runs the shelters.

As many as 10 percent of the 4,100 beds in nonprofit-run, Tier 2 shelters are vacant, according to Donna Galeno of the American Red Cross. One shelter for pregnant women run by the Henry Street Settlement in lower Manhattan has 35 empty beds out of a total of 75. And a shelter-based job training program designed to provide housing for 33 families is only three-quarters full, said Rita Zimmer, executive director of Women In Need, a shelter provider. Meanwhile, the city also continues to house many families in substandard welfare hotels.

“There are families who need to be in these facilities and should not be in hotels. They could be receiving child care, counseling, job training and all the other programs we provide,” said Zimmer. About 5,750 families are living in the city’s homeless shelter system Nearly 1,000 live in hotels, many of them run by for-profit landlords, and about 300 of those are non-compliant with city laws regulating shelter.

The vacancies appear to be the result of a new city rule implemented last August that prevents families from entering the shelter system if investigators determine they have housing options in doubled-up apartments with friends or family. Women In Need and Henry Street both report that some families are entering their shelters only to be promptly removed by the city and returned to assessment centers–presumably deemed ineligible for shelter.

On August 3, the city began refusing shelter to families who have recently lived doubled-up in apartments with friends or relatives, arguing that these families have alternatives to the shelters. Last month, a court-accredited monitor of the city’s family shelter system confirmed what most advocates have long suspected: that many truly desperate homeless families are being denied shelter because the city arbitrarily decides their plight is not quite desperate enough.

The study, by medical anthropologist Anna Lou Dehavenon, is based on lengthy interviews with a random sampling of 122 families at the Bronx Emergency Assistance Unit (EAU). Of those families surveyed since last August, the majority had returned repeatedly to the Bronx office because they were in dire need of housing–only to be rejected again.

All but two of the 22 families Dehavenon interviewed after the policy started said they were “denied shelter repeatedly” and had instead slept in subways, building hallways, hospital emergency rooms–or had sneaked back into the EAU.

Department of Homeless Services officials responded that they don’t reject shelter applicants without a thorough investigation of each case. But last month, state Supreme Court Justice Helen Freedman criticized the city’s system and ordered a more thorough effort in assessing eligibility.

Asked about the high shelter vacancy rate, Department of Homeless Services spokesperson Susan Wiviott said she could not comment. She said, however, that the city was already complying with the law before Freedman’s order. “We are trying to be sure that a very expensive and very scarce resource is available to the people who most need it,” she said.