The parking inspectors' union says this figure is the "tip of the iceberg".
Australian Services Union representative Lita Gillies urged drivers to contest fines in court because the accuracy of underground sensors installed in 4600 of the city's parking bays was uncertain.
There are allegations parking inspectors have been ordered to book up to 350 drivers a day as the council tries to recoup millions of dollars lost as a result of bungled parking reforms.
Ms Gillies said teams of about eight inspectors had been given quotas to book 250-350 motorists a day in order to meet budgets.
"The only winner out of the whole situation is the council, who get to plan how they will spend the revenue," she said.
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"If 10,000 (fines) have been withdrawn, it is just the tip of the iceberg.
"There will be many more members of the public who will not be contesting because they will be under the assumption that they have been correctly fined."
Figures from the City of Melbourne reveal that in 2011-12, nearly a third of disgruntled motorists who appealed to council against their fines had them overturned.
Of 31,400 contested fines, more than 10,800 were scrapped.
The council's budget, delivered in May, revealed an $8 million black hole.
The council's former parking manager had predicted new parking fine technology would reap an extra $6 million. The council issued 383,000 fines in 2011-12.
A council spokeswoman said while there was an expectation that a certain amount of money would be raised through fines, she denied parking inspectors had been given quotas for booking drivers.
"While it is a parking officer's role to maximise the detection of illegally parked vehicles, it is important to note that the number of fines issued is determined by the behaviour of drivers," she said.
"Any service develops a revenue budget. City of Melbourne's parking and traffic revenue budget is built largely on precedent, and includes the expectation of money raised through fines.
"If requested, daily or weekly reports are provided showing measures of revenue generation."
The spokeswoman said it was "completely untrue" that fines issued using the underground sensor technology were being overturned.