Agencies who help the homeless are complaining the city is woefully behind in paying them.
But the city blames the nonprofits for paperwork errors and not doing what they promised.
Meanwhile, the Institute for Human Services and Gregory House say they need the money to operate and that the city delays are holding up a significant portion of their income.
At Gregory House, people living with HIV and AIDS get affordable housing assistance.
Its executive director says they need consistent cash flow.
"In this case, these are rents that we're committed to housing folks and keeping them from being homeless." said director Jonathon Berliner.
Berliner said about 33 percent of his budget comes from HUD grants administered by the city.
But right now, he said the city is four to five months behind in paying them and Gregory House is owed about $225 thousand. He calls it a chronic problem.
"We're at a point where I'm trying to get a line of credit with a bank. We've never had to do that," he said.
The Institute for Human Services has the same complaint, but with a bigger deficit.
"Right now it's over $1 million," said Executive Director Connie Mitchell, adding that 58 percent of her budget comes from the city.
She added that the million dollars is enough money to pay for a whole month of homeless programs and housing subsidies.
"So if we don't get paid then we are floating our operations for that amount of time," Mitchell said. "When we're paying rents for people and we don't get paid for the rents it's very hard for us to carry that sometimes."
The city disputes the amount IHS says it's owed, and said the nonprofit is to blame for the payment problems.
"Some invoices were incomplete, most were very late, and they were all submitted at once, delaying the process further," the city said. The city Department of Community Services "is required to protect taxpayer dollars by substantiating all invoices."
At the Gregory House, there's hope that a fundraiser set for Sept. 9 will help alleviate their funding fears.
The city, meanwhile, says it's up to date with Gregory House payments -- but that's news to Berliner.
"We get various excuses. There's always pointing the finger elsewhere." he said.
Added Mitchell, "I think we, fundamentally, have to look at how government reimburses non-profits for the work that we do."