If the warehouse shelter doesn't happen, the San Diego Housing Commission would like some money back

The San Diego Housing Commission is not happy.

It also sees a potential fix.

If a recent proposal to turn an empty warehouse into a giant homeless shelter fails, a project that would require large sums from multiple sources, perhaps even the commission, the agency is formally asking that its budget not be slashed.

"This decrease in City funding" may "have significant impacts" on "the most vulnerable San Diegans," a majority of the commission's board wrote Wednesday to council members. Without millions of dollars the agency had been counting on, we "will need to reduce or, in some cases, eliminate some vital programs."

The letter puts into writing what many officials had already been saying publicly , that the mayor's plan to increase homelessness services in one area could hurt others, and turns the spotlight on council members facing a range of tough calls about how to address a deficit.

The mayor's original proposal called for reducing the commission's budget by more than $20 million, amounting to around a 42 percent cut.

That came around the time Mayor Todd Gloria announced a proposition to turn a vacant building near the airport, at Kettner Boulevard and Vine Street, into a 1,000-bed facility.

The region unquestionably needs more spots for homeless residents . Yet details of the arrangement, including a possible $1 billion-plus price tag over the next 35 years, appear to have slowed the approval process and many housing commissioners think there's at least a chance the effort flounders.

If the proposal does stall, at least in its current form, the agency asked the City Council to give back $18 million in order to "fully fund" its $52 million financial plan for the coming fiscal year. (Council members approve the budget, although the mayor does have some veto power.)

There are two areas worrying housing leaders.

The commission oversees about a dozen facilities around San Diego, including several downtown run by Father Joe’s Villages and Alpha Project, and the letter said more money was partially needed to "continue operations at City homeless shelters."

But there's also the agency's work preventing homelessness from happening in the first place.

More people lost a place to stay for the first time than the number of homeless people connected to housing during every month of the past two years , and officials countywide are increasingly trying to slow that trend by helping low-income residents cover rent .

When a state audit recently slammed how California tracks homelessness spending, rental assistance was one of the only initiatives singled out for praise.

The commission manages multiple Housing Choice Voucher programs. Even if the city gave everything asked, continuing paying for those vouchers was already complicated by the region's sky-high rents and federal funding wasn't covering expenses, according to the letter.

The city council president said he was open to changes.

"I will be carefully weighing the potential consequences of the proposed reductions to the Commission’s budget," Sean Elo-Rivera said in a statement. "While I understand the City’s lack of revenue will make for difficult choices, we simply cannot afford unnecessary cuts to programs that prevent homelessness."

The Mayor's Office has acknowledged budget constraints while saying everybody needs to dig deep for solutions.

"Whether it’s at the Kettner and Vine site or elsewhere, we fully intend to open a new large shelter in the coming year and will need to plan for funding accordingly," spokesperson Rachel Laing wrote in an email.

Both sides pledged to keep negotiating.

Five commissioners signed the request. Stephen Cushman abstained and Kellee Hubbard was absent during the April 12 meeting that voted on sending the letter.

The City Council will continue debating the budget during all-day sessions May 1-3 and again May 6-7. Members of the public can weigh in the morning of June 7 before a council vote later that month.

The new fiscal year begins July 1.

Staff writers Jeff McDonald and David Garrick contributed to this report.

This story originally appeared in San Diego Union-Tribune .