The teacher evaluation battles are not over yet.

Hundreds of school districts across New York pushed to get their teacher evaluation plans approved in time to meet Gov. Andrew M. Cuomo’s Jan. 17 deadline, so that they didn’t lose their increase in state aid.

But several districts, including Buffalo, quietly agreed with their unions not to use the evaluations as grounds for teacher terminations.

State Education Department officials say they were unaware of those agreements when they approved the districts’ evaluation plans. If the districts do not revoke those agreements, they will lose millions in state and federal funds, state officials said.

“There can be no side agreements,” State Education Commissioner John B. King Jr. said in a recent interview. “If there are conflicting agreements, their state aid [increase] will be invalidated.”

For Buffalo, this appears to call into question the status of more than $30 million in state aid this year, in addition to more than $10 million in various other government funding this year and tens of millions in future years.

It’s not clear how many districts in New York have negotiated such terms with their unions. King, as well as Buffalo Teachers Federation President Philip Rumore, alluded to “a number of districts” having such arrangements, but neither would say how many or identify the others.

The agreements, such as the one in Buffalo, to not use the evaluations in termination proceedings were documented in letters between the two parties that were not submitted to state officials as part of their evaluation plans.

State officials say they became aware of what they call the “side agreements” only after the state approved the evaluation plans.

King says the agreements violate the intent of the law.

“The law says the evaluations ‘shall be a significant factor in employment decisions,’ ” the commissioner said.

Union leaders disagree, and emphasize another passage in the law. “That interpretation is wrong. The agreement is permitted under the law,” said Carl Korn, a New York State United Teachers spokesman. “The law says the district ‘may’ bring charges [after two years of ineffective ratings].”

In Buffalo, two days before the district submitted its evaluation plan, Superintendent Pamela C. Brown signed a letter to Rumore promising not to use evaluations from 2011-12 or 2012-13 in employment decisions.

“I am writing to confirm the district’s commitment to ensure that all teachers who are subject to the new [teacher evaluation plan] will not be negatively affected by the results of their evaluation ratings for the 2011-12 and 2012-13 school years,” she wrote in the letter, dated Jan. 15.

The superintendent, in her letter, specified that the district will not pursue termination proceedings against any teacher based on a rating of “ineffective” for either of those years.

“The district understands that it would not be fair to our teachers to use this process against them during this early stage of implementation,” Brown wrote.

Buffalo submitted its evaluation plan to the state Jan. 17 and received a quick approval.

In a letter to Brown dated Jan. 29, a state Education Department official cited the superintendent’s letter to Rumore, a copy of which Brown had apparently provided to the state at some point after the district submitted its plan.

The state does not consider that letter to be part of the district’s annual professional performance review plan, wrote Julia Rafal-Baer, executive director of the state’s Office of Teacher and Leader Effectiveness, Policy and Programs.

“Accordingly, the department considers void any other previously signed agreements between and among these parties and does not recognize any such agreements as part of the Buffalo Public Schools’ approved Jan. 17, 2013, plan,” Rafal-Baer wrote.

The state reserves the right to revoke its approval of the district’s plan, she wrote – and if that happens, the district stands to lose not only its $33 million increase in state aid, but nearly $14 million in various other funding, she wrote, and could jeopardize tens of millions in additional funding.

In a follow-up letter to Brown on March 25, Rafal-Baer again expressed the state’s objections to the agreement between the district and the BTF.

The state does not consider that agreement to be part of Buffalo’s teacher evaluation plan, Rafal-Baer wrote.

“The department considers void any other previously signed agreements between and among those parties,” she wrote. “The Buffalo Public Schools must implement the terms of its approved [annual professional performance review] plan.”

In response to questions from The Buffalo News, district spokeswoman Elena Cala initially said Brown was too busy to talk about teacher evaluations and directed questions to Associate Superintendent Debra Sykes.

Cala later said Brown wanted to be the person to discuss the agreement. The superintendent, however, did not follow through on a scheduled interview Thursday. A statement from Brown was subsequently emailed Saturday afternoon.

It stated in part: “The District is committed to implementing the approved plan with fidelity and in compliance with all relevant federal and state laws, regulations and rules. Those laws require the District to consider teacher and principal ratings in decisions relating to promotion, retention, tenure determination, termination, and supplemental compensation.”

It went on to state “all federal and state laws, regulations and rules will be taken into consideration” when determining disciplinary action against teachers.