The New York City Housing Authority’s handling of apartment vacancies and renovations results in the loss of millions of dollars in potential rent paid to the city, according to an audit released yesterday by the city comptroller, William Thompson Jr.

The audit, covering six city housing developments in Manhattan, Brooklyn, and Queens between June 1990 and December 2005, found that, on average, 18% of the units were vacant and off the rent roll for 40 months during that period. Had Nycha reduced the vacancy lengths by 20%, or eight months, more than $4 million a year in additional rent would have been collected, the audit concluded.

In a letter to the comptroller’s office, Nycha’s general manager, Douglas Apple, said the audit overestimated the potential revenue and failed to account for the maintenance and utility costs of active units, but that the authority has recently or will shortly heed the audit’s recommendations.

Mr. Thompson called Nycha’s management of the apartments “unacceptable and totally fiscally imprudent,” adding that it “needlessly disrupted” current residents’ lives and “deprived” those looking for housing.

Citing Nycha’s $2 billion investment in its 179,315 units that house 413,817 residents, Nycha’s chairman, Tino Hernandez, said in a press release yesterday that the audit “doesn’t fully reflect the extensive preservation efforts under way by the City and the New York City Housing Authority.”

The city housing agency, which is the largest in the country and represents 8.6% of all city housing, and Mayor Bloomberg often use the authority’s overall 2% vacancy rate as a beacon of its efficiency. Mr. Thompson said the number was “laudable,” but insisted that “at the same time something’s wrong.”

A community housing activist, Bertha Lewis, said in a statement that Nycha should allow all of its records to be audited, and said that if the authority addressed the excessive vacancy problem the money gained would allow it to stop “raising rents and fees on tenants.”

The comptroller also released another audit that condemned Nycha for not integrating its two computer systems, leaving them open to critical mistakes and manipulation.

The audit found that 3,920, or 10%, of the eligible applicants were not transferred to the waitlist, meaning that they may have missed out on housing when it was available to them.

On March 1, Nycha sent out requests for proposals that called for the integration of the two interfaces. Nycha said it expects the integration to be completed by the second half of 2007.