The Federal Aviation Administration announced Friday that it grounded a Hawaii cargo airline after one of its Boeing 737 jets crashed into the ocean this month. The agency said an investigation into maintenance and safety issues had found deficiencies.

The FAA said it had been investigating Rhoades Aviation, which does business as Honolulu-based Transair, since last fall and proposed grounding its planes June 13, about two weeks before the crash. The airline had 30 days to contest the proposal and asked the agency to reconsider, which it declined to do.

The FAA said the decision to bar the carrier from flying was made separately from the investigation into the crash.

The 45-year-old 737 splashed down off the coast of Hawaii in the early hours of July 2, shortly after taking off from Honolulu, bound for Kahului Airport on Maui. The plane lost engine power and unsuccessfully tried to get back to land. Both pilots, the only people aboard, were rescued by the Coast Guard and Honolulu Fire Department. The pilots were in stable condition when they arrived at a hospital.

In a statement, the FAA said Friday that it has removed Rhoades Aviation’s authorization to conduct safety inspections effective midnight Thursday Hawaii time. Without that authorization, the carrier cannot legally operate, the agency said. The FAA didn’t specify what problems it found but said the airline would not be able to fly again “until it complies with FAA regulations.”

A company representative did not respond to a request for comment.

The airline’s website indicates it has been in business since 1982 and operates between all the state’s islands. The FAA said that as of Friday, the company had a single operating 737-200, one of the oldest variants of the jet.

A sister company to Rhoades operates a separate fleet of turboprop Short 360 aircraft under the Transair brand. The FAA said that business was not affected by the order.

The National Transportation Safety Board is leading the investigation into the crash. The NTSB said this month that the plane was badly damaged and sank into the Pacific Ocean. The agency used sonar to locate the jet and released video of the cabin resting on the ocean floor.

Investigators said they also planned to interview the pilots. Christopher O’Neil, a spokesman for the NTSB, said the board’s investigation of the crash will examine the FAA’s oversight. O’Neil said the recovery of the 737 is paused while the team comes up with a plan.

The pilots of a Boeing 737 cargo jet were rescued on July 2 after making an emergency landing in the ocean off the Hawaiian island of Oahu. (DVIDS/U.S. Coast Guard District 14 Hawaii Pacific)

In air traffic control recordings, the crew can be heard struggling to get the plane back to Honolulu’s Daniel K. Inouye International Airport.

“We’re going to need the fire department,” one pilot told an air traffic controller. “There’s a chance we’re going to lose the other engine, too. It’s running very hot.”

The controller soon warned the pilots the plane was dropping: “Low altitude alert. Low altitude alert. Are you able to climb at all?”

“No. Negative,” the other pilot responded.

Boeing 737s can fly on a single engine, and it is rare for a plane to suffer a problem that knocks out both. The NTSB is unlikely to issue its findings for months. The investigation will consider the role played by the pilots, air traffic controllers, weather and the plane itself.