A plan to clean up a toxic waste site and build four schools on it in the Bronx could be jeopardized if the City Council votes today to delay it, Mayor Bloomberg’s top aide on education said.

Deputy Mayor Dennis Walcott, who said he is “without question” satisfied the Mott Haven site will be safe, said yesterday that scuttling the project would deprive the city of thousands of badly needed classroom seats.

But opponents, including several members of the council, said the site could put students at risk.

“The fact is, it’s irresponsible to approve a school site that may be dangerous to kids,” an attorney for a coalition of organizations opposed to the plan, David Palmer, said.

The project has already been delayed once, in December, following an outcry by activists.

To mollify opponents, the Bloomberg administration agreed to fund a $9,500 independent analysis of the plan, to be completed by the end of the month.

Still, Mr. Walcott said state and municipal environmental regulators have approved the plan, which includes $30 million to detoxify the land. He promised to give serious consideration to the independent contractor’s findings and revise the cleanup as necessary.

Eleventh hour negotiations between the administration and the City Council were to continue through the night, Mr. Walcott and a Queens council member, Leroy Comrie, said separately.

Mr. Walcott said if the plan, which would add a total of 2,400 students in two high schools, a combined middle and high school, and a charter school, is defeated today, costs for a new plan could rise — if it even gets enough support to succeed.

Mr. Palmer noted that the consultant has already identified five preliminary ways to “make the cleanup more protective.”

“I think there’s a lot of deal-making going on behind closed doors that we’re not invited to,” he said. “I’m worried that the council will make a deal, and I think it would be irresponsible if they did at this point.”

To go forward, the construction plan needs to pass three sets of votes beginning this morning, including a final one by the entire 51-member council.