Bloomberg said he was "very disappointed" and blasted the ruling for relying on "archaic Washington regulations" that keep New York and other cities "from choosing to create cleaner air." He said the city was exploring options to appeal.
Last month, the Metropolitan Taxicab Board of Trade, a trade association claiming to represent a quarter of the city's cabs, sued to block enforcement of the rules.
The plaintiffs argued that only the federal government, not the city's Taxicab & Limousine Commission, has the authority to regulate emissions and fuel efficiency standards.
In addition, they claimed that hybrids aren't safe enough for use as cabs, which take a beating on city streets.
Trade association president Ron Sherman praised the decision.
"Millions of people who ride taxicabs and the thousands of drivers, owners and other participants in the New York City taxi industry can breathe a sigh of relief today," he said.
The new rules would have gone into effect Nov. 1 and required any new cab coming into service to achieve a fuel efficiency standard of 25 miles per gallon. The following year, that would have increased to 30 miles per gallon.
The standard yellow cab, the Ford Crown Victoria, gets about 14 miles per gallon while some hybrid models, which run on a combination of gasoline and electricity, achieve as much as 36.
The city sells licenses to drivers and operators, who must purchase vehicles that meet the taxicab commission's specifications.
There are more than 13,000 taxicabs in New York City, and nearly 1,500 are hybrids.
The majority of those were purchased voluntarily by medallion owners, but several hundred were mandated through the sale of medallions that were specifically earmarked for alternative fuel vehicles.
Without ruling on the merits of the case, U.S. District Judge Paul A. Crotty temporarily blocked enforcement because he said the plaintiffs would suffer irreparable financial harm if they were forced to comply with the rules by the deadline.