Norton-Perry said it was inappropriate to renew Fleager's agreement considering the council will soon have new members.
Norton-Perry and Councilman Art Bennett's seats were both up in November. Norton-Perry chose not to seek reelection, but Bennett did and he won his seat back.
Newcomer Cynthia Moran was voted in and will fill Norton-Perry's spot.
Bennett and Moran are expected to be sworn in as council members at the next meeting.
Councilman Bill Kruger resigned in September. His resignation came to the council too late and forced the city to hold a special election in March to fill it.
Council members met in closed session last month to negotiate a potential amendment to Fleager's contract.
At Tuesday's meeting, councilmen Ed Graham, Peter Rogers and Bennett approved the agenda item that extended Fleager's contract to Nov. 30, 2014.
This was an 18-month extension to Fleager's contract that was originally set to expire May 31, 2013.