Twenty-three councilors approved of Vilnius Mayor Remigijus Šimašius' decision to dismiss Vaitkunskienė from office, 24 voted against it and one ballot was declared invalid.
Simasius on Wednesday proposed Povilas Poderskis, his current IT adviser, for the post of the municipality's director of administration.
The council rejected the opposition's proposal to postpone the decision until the next meeting.
Simasius admitted that Vaitkunskiene had played a key role in getting the city's debts under control, but criticized her for poor management, a destructive attitude toward teamwork and personnel management, and blocking of progressive decisions.
The mayor said that he had changed his opinion about the director of the administration due to "lies, manipulations and unethical moves to keep the post" over the past two weeks.
Vaitkunskienė says that Šimašius and those around him do not like her principled stance on the use of budget funds and accuses the mayor of putting pressure on her to resign.
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