Judge Martin Feldman of the US District Court in New Orleans granted a preliminary injunction against the moratorium, finding it overly broad and insufficiently justified.
The administration would appeal the ruling, White House spokesman Robert Gibbs said.
Hornbeck Offshore Services and other Louisiana-based oil services companies, which provide ships and other services to oil companies, had argued in court Monday that the Obama administration's six-month moratorium on drilling oil wells in the Gulf of Mexico would irreparably harm their businesses.
Feldman said in his ruling that the administration's review of drilling did not sufficiently prove a need for such a broad moratorium, did not provide a timeline for implementing changes to safety aboard drilling rigs and did not sufficiently clarify what constituted deepwater drilling.
"If some drilling equipment parts are flawed, is it rational to say all are? Are all airplanes a danger because one was? All oil tankers like Exxon Valdez? All trains? All mines? That sort of thinking seems heavy-handed, and rather overbearing," he wrote.
The court found the government had not sufficiently shown the need for "a blanket, generic, indeed punitive, moratorium" rather than one more tailored. Feldman said the companies involved in the suit had shown they were likely to suffer irreparable harm from the decision.
"An invalid agency decision to suspend drilling of wells in depths of over 500 feet simply cannot justify the immeasurable effect on the plaintiffs, the local economy, the Gulf region, and the critical present-day aspect of the availability of domestic energy in this country," he said.
The moratorium extended in May for six months covers new deepwater offshore drilling and halted permits and active exploration of drilling opportunities off coastlines in Alaska and Virginia and in the Gulf of Mexico.
"The president strongly believes ... that continuing to drill at these depths without knowing what happened ... does not make any sense and ... potentially puts (the) safety of those on the rigs and safety of the environment in the gulf at a danger that the president does not believe we can afford right now," Gibbs said.