The Reagan administration has agreed to delay a plan that could remove thousands of vacant apartments from the nation's public-housing stock, but officials say they are determined to pursue the idea in a second Reagan term.

The Housing and Urban Development Department has published a proposed regulation that would cut off operating subsidies for many of the 40,000 vacant public-housing units, unless federal aid is committed to restore them. Since HUD also controls the federal modernization money, critics say the department could use the new authority to shrink the scope of public housing.

"It is a pernicious attack that could basically drive these units to demolition, which a lot of people think is the underlying strategy," said Gordon Cavanaugh, an official with the Council of Large Public Housing Authorities.

But Warren T. Lindquist, HUD's assistant secretary for public housing, said the goal was to restore as many units as possible to livable condition while ending federal aid for those with no hope of rehabilitation.

"I know they're suspicious and they don't believe it, and there's not a hell of a lot I can do about it," Lindquist said of his critics. "But I want to make this damn thing work."

The proposal is one of a host of politically sensitive issues -- from combating acid rain to revamping disability benefits -- that the administration has put off until after the election. Lindquist said the regulation had been delayed until early next year because of strong criticism from Congress and local housing officials.

"It was not pulled because of the election year," he said. "It was pulled because it would not make any sense to ram it through . . . . The feelings against this were very strong."

Advocates on both sides agree that soaring vacancy rates are a severe problem. For reasons ranging from mismanagement to neighborhood deterioration to lack of funds, local housing officials have allowed units to remain empty for months or years, even as their waiting lists grow.

According to HUD, Newark's vacancy rate is 34.6 percent, followed by 27.3 percent in Dallas, 23.9 percent in Detroit, 23.3 percent in Providence, R.I., 19.4 percent in Cleveland and 19.1 percent in Boston. These financially ailing housing authorities -- along with the District of Columbia, where about 1,400 of the 12,000 public housing units are vacant -- could lose millions of dollars under HUD's plan.

The proposal would allow housing authorities a 3 percent vacancy rate and eliminate federal aid, except for heating and security costs, for the remaining vacancies. HUD would exempt only those units that were scheduled for repairs.

Seventeen House members, led by Reps. Henry B. Gonzalez (D-Tex.) and Barney Frank (D-Mass.), told HUD in June that the plan would have "a potentially devastating impact" on public housing. They said that HUD had been unable to estimate how many vacant units might be restored and that the plan amounted to "penalizing public-housing authorities for HUD's failure to fund sufficient comprehensive modernization applications."

Housing advocates say that HUD's $1.5 billion modernization budget is enough to finance only a fraction of the projects that need renovation.

"You need to give public-housing authorities the tools to solve the problem before you cut them off at the knees," a Gonzalez aide said. "HUD didn't even consider the normal turnover period. If a family moved out, HUD could declare the unit vacant the next day."

Lindquist said the revised plan would reflect some of the criticism, but that the problem was not simply a lack of federal aid. He said that Newark, for example, had more than $50 million in unspent federal modernization funds.

Newark housing official Joe Sweeney said the city was moving to spend that money, but that it would take $200 million more to restore its 4,000 vacant units. He said it was "hogwash" to blame Newark for the vacancies because the city had consolidated some half-empty and poorly designed projects at HUD's request to save energy.

Lindquist acknowledged that it would take substantial federal outlays to restore many of the vacant units across the country.