Three Royal Australian Navy crew members have been rescued with minor injuries after their helicopter ditched in the Philippine Sea.

The navy's MH-60R Seahawk fleet has been grounded after a helicopter got into difficulty and made an emergency landing on Wednesday night.

Three crew members sustained minor injuries and were rescued by boats dispatched by HMAS Brisbane.

Defence Minister Peter Dutton says an investigation is being conducted into what went wrong.

"It got into difficulties, they're not sure yet what went wrong but the most important thing is that the crew members were rescued ... and they were brought back onto the vessel about 20 minutes later," he told 2GB radio on Thursday.

"So minor injuries, their families have been notified, but I guess it just underscores the difficult work and the dangerous work that the men and women of our Australian Defence Force undertake."

Commander of the Australian Fleet, Rear Admiral Mark Hammond, confirmed the MH-60R Seahawk fleet had been temporarily grounded during the investigation.

"With the aircrew safe, investigating the circumstances that led to the helicopter ditching is the priority at the moment," he said in a statement.