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SAN FRANCISCO — Amid concerns about marine life, a federal judge temporarily has blocked the U.S. Navy from deploying a new high-frequency sonar system used to detect enemy submarines. 

Magistrate Judge Elizabeth D. Laporte, however, said Thursday that the Navy may use the sonar during wartime and must be allowed to train with it beforehand. Given that, the magistrate ordered both sides back to court Nov. 7 to begin formulating a plan balancing environmental and military concerns. 

The case stems from a lawsuit by the Natural Resources Defense Council and other environmental organizations that sought to stop the Navy from training in most of the world’s waters with a powerful sonar system the groups maintain can strand, harass or kill marine mammals. 

“It is undisputed that marine mammals, many of whom depend on sensitive hearing for essential activities like finding food and mates and avoiding predators, and some of whom are endangered species, will at a minimum be harassed by the extremely loud and far-traveling ... sonar,” Laporte wrote in her lengthy ruling. 

On the other hand, she added, the Navy demonstrated that the new technology “is likely to significantly increase our ability to timely detect very quiet submarines.” 

Pauline Storum, a Navy spokeswoman, said the government was “reviewing the decision” and declined further comment. 

The Navy was planning to immediately begin testing the system throughout the world and had previously agreed to exclude polar waters and areas within 12 miles of any coast. 

“We want the tests carried out far away from coastlines, those are among the richest and most diverse areas,” said Joel Reynolds, an NRDC attorney. “Areas we would certainly favor is where there’s very small numbers of marine mammals, and ones where it is unlikely to do serious harm, such as away from feeding, migrating and breeding areas.”