A staffing shortage at the Big Apple’s biggest housing agency is slowing down plans to develop and build badly needed affordable apartments, which advocates charge is further compounding the city’s decades-long shortage.

The division of the Department of Housing Preservation and Development charged with the construction of new affordable apartments has lost 12 percent of its staff since the coronavirus pandemic hit and is now 24 percent under budget headcount.

Things are hardly better at the division tasked with renovating and protecting the city’s existing stock of roughly 1 million rent-stabilized units, which has lost 7 percent of its staff since COVID and is now 18 percent under budget.

“It means they can develop less-affordable housing,” said Brendan Cheney, the top spokesman at the New York Housing Conference, which conducted the staffing review.

“It means projects that are coming to them now, they have to wait a long time before they can really work on them and get them online,” he said, adding that makes “the project more expensive for the city.”

Cheney said that better pay and more flexible working arrangements offered by private-sector employees were helping to fuel the exodus of HPD project managers and lawyers who would typically shepherd projects through.

It’s another hurdle that builders in New York must contend with in addition to the Big Apple’s complex zoning regulations, lengthy and oft-contentious neighborhood involvement requirements and the City Council’s typical deference to local lawmakers when deciding what projects ultimately move forward.

Just 407,000 new units of housing were permitted between 2001 and 2018, while employers created another 770,000 jobs across the five boroughs, city data shows.

That ratio becomes even more skewed if the job losses sustained during Wall Street’s 2009 collapse are excluded.

“I’ve inherited a broken city with broken systems and we can either put a band-aid on top of these broken systems, or you can go to the core and fix them. I’m going to the core to fix them,” Adams told The Post in a statement.

HPD did not immediately respond to request for comment.