Plans for a 195-unit apartment complex on Second Avenue in Waltham are in limbo as city officials continue to fight a project they say should not be built under the state’s affordable-housing law.

Officials contend that the city already meets the state’s threshold for affordable housing, and are concerned that the project is too dense and not in an area suitable for a large-scale residential development.

But the state recently rejected the city’s affordable-housing inventory calculations, and a spokesman for the Phoenix-based developer, Alliance Residential, said it is confident the project will move forward.

“Alliance is looking forward to working with the city, being a good neighbor and finding ways to work together,’’ said Tim West, an Alliance spokesman.

In December 2015, the city’s Zoning Board of Appeals denied Alliance’s application for a comprehensive permit to build 146 market-rate apartments and 49 affordable rental units at 341 Second Ave. The decision was based on the city’s belief that the subsidized housing inventory in Waltham comprises more than the state minimum of 1.5 percent of the total land area.

The city says that eligible housing accounts for 1.6116 percent of its total land area. But the developer claims that the city double counted its deduction for water bodies, and thinks the inventory is 1.15 percent.

The state Department of Housing and Community Development recently rejected the zoning board’s position and sided with the developer. The letter states that the developer “has raised multiple issues that raise legitimate concerns about the board’s calculation and analysis . . . ’’

Mark Hickernell, a member of the Zoning Board of Appeals, said the city will appeal the state agency’s decision and the project will be on hold until a final ruling.

He said Catherine Cagle, the city’s planning director, told the board on Feb. 17 that she is confident in the city’s calculations.

Cagle did not return calls seeking comment.

Hickernell said city officials would prefer not to go through the comprehensive permit process allowed under the state’s affordable-housing law because they don’t have as much input as they would during a typical review.

Hickernell said the City Council has raised serious concerns about the project.

In a letter to the zoning board, the council says that the project is in a commercial zoning district with limited access to public transportation. The letter says the project is too dense for the acreage and does not provide enough parking.

The project calls for 195 apartments — 30 studios, 67 one-bedroom, 78 two-bedroom, and 20-three bedroom units. Amenities include an indoor pool, fitness center, dog park and grooming center, a high-definition theater, and a game room/lounge.

West said the developer believes the project will provide much-needed affordable housing options to support commercial growth taking place in neighboring parts of the city. Under the affordable-housing law, the developer must rent at least 25 percent of the units at affordable rates.

Jennifer Fenn Lefferts can be reached at jflefferts@yahoo.com.