At least six patrol boats used by the Royal Australian Navy to intercept asylum seekers have been docked at the Darwin Naval Base amid concerns over structural cracks.

The large cracks were found near the engine room of one of the Armidale-class patrol boats about 10 days ago, according to a report in The Australian newspaper.

It is not the first time cracks have been found in the boats.

The Navy ordered a review of the Armidale class in August 2012 to assess whether the cracks were part of a fleet-wide design problem.

A spokesman for Immigration Minister Scott Morrison says the "maintenance issues" are being addressed.

"The Defence Materiel Organisation, the Armidale-class patrol boat in-service support contractor (DMS), and the ship's builder and Design Authority (Austal) are addressing the issue," he said in a statement.

"Maintenance issues such as this are not unexpected when operating a significant number of maritime assets in a wide range of demanding environments.

"However, the situation has been exacerbated as a result of the previous government's failure to protect our borders, which saw our Navy and Customs and Border Protection run a non-stop water taxi service to Christmas Island for five years."

The spokesman says Operation Sovereign Borders has not been affected by the docking.

"Any vessels that seek to illegally enter Australia will be intercepted and safely removed from our waters," he said.

"The Australian Customs and Border Protection Service and Australian Defence Force collaborate closely to ensure that at all times, appropriate assets are made available to Border Protection Command for maritime security operations."