The controversial Absent Teacher Reserve is set to become even more expensive for New York City as educators in the pool build years of experience and earn bonuses.

That’s according to a report released Thursday by the nonpartisan Citizens Budget Commission, which estimates the reserve will cost $136 million this school year.

The reserve is comprised of teachers who don’t have a permanent position because their schools were closed, or because they face legal or disciplinary problems. Many serve as roving substitute but others do deskwork or administrative tasks — or, critics say, nothing at all — while collecting a full salary.

The commission dug into the costs of the reserve just as the city’s contract with the United Federation of Teachers is set to expire in November, and the report adds to calls for the city to negotiate major changes regarding teachers in the pool.

“We as taxpayers have to ask: Are we going to ensure their payment and job protection indefinitely?” said Maria Doulis, Vice President of the Commission. “I think, for most people, that answer is no.”

But that is easier said than done, with the union fighting hard to keep job protections for its teachers. In response to the report, a UFT spokeswoman said that the commission should be “checking its numbers” and argued the reserve actually saves the Department of Education money.

“Teachers are assigned to schools to replace other teachers out on medical or other leave, which allows the DOE to save tens of millions of dollars each year on the cost of hiring long-term substitutes,” the union said in an emailed statement.

Here are highlights from the commission’s report.

The average ATR is more experienced and earns a higher salary than other teachers.

Teachers in the reserve have an average of 18 years of experience and earn a salary of $98,126, according to the committee. Across the system, teachers are slightly less experienced, with about 10 years in the classroom, and make $84,108.

The report finds that paychecks have increased for teachers in the reserve, compared with city figures that were released in summer 2017. Ana Champeny, who oversees city budget analyses for the committee and authored the ATR report, said that’s likely because educators continue to collect salary boosts and bonuses just like any other teacher.

“That’s increasing the cost to the city,” she said. “And it’ll get even more expensive as more raises are awarded.”

In the meantime, a 3 percent salary increase goes into effect this week, under the terms of the city’s current contract with the UFT. With the boost, educators with 18 years of service will earn an extra $14,084 total.

Still, the commission’s report found that the Absent Teacher Reserve overall will cost less than previous years. Figures from the Independent Budget Office show that the city spent almost $152 million on the pool in the 2016-17 school year — $16 million more than this year’s estimate. The reduction could be because there are about 100 fewer educators in the reserve this year compared with Oct. 2016.

The city has saved millions through efforts to drain the reserve.

The reserve was created under former Mayor Michael Bloomberg in a bid to give principals more control to hire their own staff, scuttling union rules that previously allowed senior teachers who were laid off by their current school to transfer into new positions.

At the beginning of this school year, the budget committee found that 1,202 teachers were in the reserve. Current Mayor Bill de Blasio has tried to cut the pool in half, partially by offering severance payments to entice teachers to leave the system.

Many teachers took a deal offered this year: A lump sum payment of $50,000. The commission found that 170 teachers opted for the buyouts — costing the city $8.5 million. Still, the city will save $23 million a year by offering the payments, according to the report.

The de Blasio administration has tried to drain the reserve in other ways, such as by offering budget incentives to principals who hire from the pool, or placing reserve educators into schools even without principal approval. The latter effort has been controversial — with some principals vowing to hide vacant positions — and not nearly as effective as the city had hoped.

While officials had planned to place 400 teachers from the pool into permanent positions, only 75 openings were filled with reserve teachers. That will generate $7 million in savings by 2020, according to the commission.

But the city should negotiate more substantial changes, the commission argues.

Cities such as Chicago and Washington, D.C., have managed to tamp down on some teacher seniority rights that critics say make it difficult to lower the number of teachers in the reserve. Both cities limit the amount of time a teacher can remain on the payroll while looking for a permanent job.

The commission said New York City should fight for similar measures, and cap a teacher’s stint in the reserve to six months. Past and present administrations have struggled to strike an agreement with the union that would significantly weaken job protections for teachers, but Doulis said that the reserve is likely a priority on the city’s agenda as the two sides hash out an agreement.

“How you get to compromise and work out a solution, that’s a different story,” she said. “But I do think it’s something that will be discussed.”