The strike, affecting 350,000 students, began when talks broke down over issues including pay and teacher evaluation.
The teachers’ union had reached an outline deal on ending their action but delegates unexpectedly voted to continue discussions for two more days.
Rahm Emanuel said the strike was “illegal” and “wrong for our children”.
He said he had sought a court injunction to bring the walkout to an immediate halt because it was over “non-strikable” issues and “endangers the health and safety of our children”.
The Chicago mayor – President Barack Obama’s former White House chief of staff – issued his statement after Chicago Teachers Union (CTU) delegates voted against suspending the strike.
The confrontation is seen as an embarrassment to Barack Obama, in his home city and in the middle of a re-election battle.
The strike is the first of its kind in the US for 25 years and is awkward for a president with close ties to the mayor.
The teachers walked out after lengthy contract talks stalled over reforms aimed at revitalizing city services. The negotiations hit deadlock over a proposed teacher evaluation process.
The CTU fears more than one in four public school teachers could lose their jobs and benefits if an evaluation of their performance based on students’ test scores goes ahead.
In a statement posted on the CTU website, 800 union delegates considered a 23-page outline deal between the union and the mayor.
Union leader Karen Lewis said “a clear majority” had voted not to suspend the strike to allow delegates two more days to hold discussions with the union’s 26,000 members. Another meeting is scheduled for Tuesday afternoon.
She had earlier said she would ask the delegates to suspend the walkout.
“Teachers and school staff will return to the picket lines of the schools at which they teach at 07:30 on Monday,” the CTU statement said.
Rahm Emanuel faced a $700 million school budget shortfall when he took office last year and he has said the contract agreed with the union will cost $295 million over four years.
Under the proposed deal published by the union:
• the evaluation system would be phased in over several years while the weighting of students’ test results in teacher-evaluations would be reduced
• teachers’ health care benefits would stay at current levels
• teachers would receive a 3% raise this year followed by 2% in the following two years
• a further increase would be included if the agreement went into a fourth year
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