U.S. District Judge Paul Crotty found that the Metropolitan Taxicab Board of Trade, an association of taxi owners accounting for about a quarter of the city's 13,000 yellow cabs, had "demonstrated a likelihood of success" in having the new rules thrown out. He granted a preliminary injunction.
Implementation of the regulations now would be costly to the taxi industry, Crotty ruled.
The city said it was considering an appeal.
"The decision is not a ruling against hybrids cabs, rather a ruling that archaic Washington regulations are applicable and therefore New York City, and all other cities, are prevented from choosing to create cleaner air and a healthier place to live," Mayor Michael Bloomberg said in a statement.
There are already about 1,400 hybrid taxis in the city, the Taxi and Limousine Commission said.
Hybrid vehicles are powered by a combination of gasoline and electricity. They emit less exhaust and have better gas mileage than other vehicles.
The original lawsuit, filed in September in Manhattan federal court, also argued that the rules had been rushed out without adequate concern for safety and cost.
"While a decision to announce the immediate change to 'clean' taxis might be politically enticing and expedient, it is also irresponsible, dangerous and illegal," the suit said.
Green taxis are a cornerstone of Bloomberg's environmental plan, which aims to curb the city's carbon footprint by 30 percent by 2030.
State legislators have defeated another Bloomberg initiative — a "congestion pricing" plan similar to one in London that would have charged drivers $8 to enter much of Manhattan.