City budget director Mark Page, one of the mayor's four representatives on the MTA board, said "the ill will arising from this proposal" would probably outweigh the expected $10 million a year in additional revenue.
MTA Executive Director Elliot Sander said he sympathized with the city's position but added, "This is an accounting issue. And it's something that we need to do given the current state of the MTA's finances."
The plan will go into effect in six weeks and affects dozens of agencies including the New York Police Department, the New York State Police and the Nassau and Suffolk county police departments.
The agencies currently use free E-ZPass fare payment tags. When the new policy takes effect, the agency vehicles will continue to use their tags but the MTA will bill the agencies for the tolls.
The policy applies to the MTA's five bridges and two tunnels.
The vote came after the MTA faced a controversy over the free use of E-ZPass tags by current and former members of its board.
Board members voted in June to give up their free lifetime passes, a perk criticized amid a financial crunch at the nation's largest mass transit agency.
