Thornton said he was "extremely troubled" that most of the affected teachers are in elementary schools.
"Children are being caught in the middle," Thornton told reporters. "They deserve better."
Anticipating the state cuts and the end to about $100 million in federal stimulus funding, the district's own budget cut school summer options and froze all "noncritical" building maintenance, Milwaukee Public Schools said on its website. Besides the 519 layoffs, the system will not fill about 500 open positions.
At a news conference, Thornton repeated his call for members of the the Milwaukee Teachers' Education Association to contribute 5.8% annually to their pensions.
The union did not return a message left by CNN Wednesday evening.
Gov. Scott Walker on Sunday signed a two-year state budget that slashes spending to local schools. The state's highest court earlier this month reinstated a bitterly contested law, pushed by Walker, that restricts collective bargaining for state workers.
Milwaukee Public Schools, which has about 82,000 students, has made $182 million in budget cuts, said communications director Roseann St. Aubin. It also closed schools, with the number going from 184 to 175.
About 71% of the system's budget goes for salaries and benefits, St. Aubin told CNN.
Several unions representing school employees agreed to pension concessions, the spokeswoman said, but teachers, who have a contract through 2013, have not formally responded. If 5,600 members were to contribute 5.8% to their pensions, the district said it would have enough to pay 200 teachers.
St. Aubin described Milwaukee at the "tipping point" in its financial support for schools. The schools want a dialogue with citizens, potential donors and supporters, St. Aubin said.
"We're going to become a smarter, more efficient district," she said.
