For most of the last two decades, financing affordable housing in New York City has been a predictable process, instrumental in adding tens of thousands of apartments for lower-income households in a city where rents continue to soar out of reach for more people every year.

But a cloud of uncertainty now hangs over those efforts, as many developers predict that projects could be choked off by the unremitting tensions between Mayor Bill de Blasio and Gov. Andrew M. Cuomo, who in January outlined a vastly expanded state role in affordable housing, one of the mayor’s signature issues.

In the latest round of city-state jousting, developers, bankers and de Blasio administration officials said they were told in meetings with aides to Mr. Cuomo that the city would lose a sizable share of up to $900 million a year that the state provides in federal tax-exempt bonds for affordable housing projects in the five boroughs.

Developers and bankers, who spoke on the condition of anonymity for fear of repercussions from Albany, said they were told that the Cuomo administration planned to use the bonds for the governor’s own recently announced $10 billion statewide housing plan.