Norton-Perry said it was inappropriate to renew the agreement considering the council will soon have new members.
Despite that, council members Ed Graham and Peter Rogers as well as Mayor Art Bennett approved the extension of the contract to Nov. 30, 2014, an 18-month extension to the contract set to expire May 31, 2013.
Norton-Perry decided this past summer to not to seek reelection. Cynthia Moran was voted in last week and will fill her seat.
Also, Councilman Bill Kruger resigned in September. A special election will be held in March to fill his spot.
Council members had met in closed session last month to negotiate a potential amendment to Fleager's contract.
"The election hadn't taken place then, and there is still another outstanding seat, and the fact that I'm leaving, I just thought it was inappropriate given the fact that his contact doesn't end until May," Norton-Perry said.
City officials said extending a contract or discussing it months in advance from its end date is standard.
If Fleager voluntary decides to leave, it would take him up to nine months to find a city manager that is comparable.
"And now he's getting close to that May deadline and he wanted to know if he could get an extension for his contact to give himself a little bit of time in the event that we were going to decide that we were not going to rehire him or extend his contact," Bennett said.
By extending Fleager's contact by 18 months, it will allow the new council to properly form their own opinions about his performance, Bennett said.
Norton-Perry's concerns are legitimate; however, they also wanted to give Fleager the courtesy of having more time to look for a job if the new council members decide they didn't want to renew the contract, Bennett said.