A cruise boat operator says he has been hit hard by marine safety authorities.

The Australian Maritime Safety Authority (AMSA) issued Broome-based company Buccaneer Ahoy a prohibition notice this week, saying it had some concerns about passenger safety.

The company is one of the first to offer low-budget cruises of the remote Kimberley coast.

The notice allegedly related to the location of the boat’s generator and its possible effect on stability.

AMSA has issued a statement saying it had received credible reports about the safety of a passenger vessel in Broome.

Senior inspectors have now toured the boat, and say that the problem with the location of a generator had been fixed, but the inspection revealed a myriad of other risks.

AMSA has issued a second prohibition notice, saying the boat could not to set sail until they had been fixed.

AMSA's national operations manager for domestic vessels Brian Hemming described the state of the boat to ABC reporters.

“The additional concerns that came up were some serious electrical safety issues, firefighting equipment that was non-functioning, watertight integrity and passenger and crew safety hatches that weren't watertight,” he said.

“These are serious safety issues for a passenger-carrying vessel and that's why AMSA takes this so seriously.”

Buccaneer Ahoy owner Doug Gould said the company has had to cancel tours for the second week in a row, and now faces losses of about $100,000.

He said AMSA had not provided enough information, and that he safety breaches were minor.

“It's very hard because they're not telling us anything ... the latest I've heard is that even though we've covered everything, when they lift the second prohibition order, they'll be placing another one on us,” he said.

He that company could have worked with AMSA on improvements, rather than suspending them outright.

“The experts that we've discussed this with say they've never, in all their years, come across anything that's been handled this badly,” he said.

But reports say the WA Transport Department has had lengthy dealings with the company, and had identified breaches of safety laws in 2015.

The Department had allegedly urged AMSA to prosecute Buccaneer Ahoy for safety issues last year.