PORTLAND – The school superintendent in Maine’s largest city has resigned in the aftermath of a multimillion-dollar budget deficit.

The Portland School Committee unanimously accepted the resignation of Mary Jo O’Connor on Wednesday night, welcoming her decision as a necessary step in addressing the district’s financial troubles and restoring confidence in the management of Portland schools.

O’Connor, who’ll receive a settlement estimated to be about $80,000, will stay on until Dec. 28 while the school committee looks for a replacement.

“For all the good she did for this district educationally, the financial problems happened on her watch and it’s disrupting the district,” John Coyne, chairman of the school committee, said after the meeting at Portland Arts and Technology High School.

City finance officials took over the school finance office earlier this month after the school finance director resigned. The amount of the school department deficit had been estimated at upward of $2.5 million, but city officials announced Wednesday it was closer to $1.7 million.

As Portland’s superintendent for six years, O’Connor oversaw the closing of four school buildings and the construction of the East End Community School.

The department instituted multicultural programs, all-day kindergarten classes, new teaching models and expeditionary learning programs at the elementary, middle- and high-school levels, including Casco Bay High School.

But many parents were outraged by the financial mismanagement. Some showed up to protest the payment of any settlement to O’Connor, whose annual salary was $120,000. Her severance package will include two additional months of regular pay, plus any accrued sick and vacation pay.

“I am a parent and a taxpayer, and the settlement should not come out of the school budget,” said Mark Usinger of Portland.