The boats out of use are undergoing maintenance, Northern Territory News reported.
Clare said the boats have been working "very, very hard" patrolling coastal waters, including the intercepting of several asylum seeker boats in recent weeks.
The boats are "under pressure (due to) the enormous amount of work these vessels have been asked to do," Clare said.
Clare met Defense Maritime Services, the Ministry of Defense's private sector partner that is providing maintenance for the patrol boats, in Darwin this week to discuss what the fleet requires and what is planned for the future, NT News said.
The number out of use is two more than the ministry had said earlier this week.
A report by The Age newspaper last month said Australian maritime authorities are stretched by now having to patrol thousands of miles of ocean around the Cocos Islands, the latest territory targeted by asylum seekers.
Since the middle of May, three boats carrying 135 asylum seekers have arrived at the Cocos, about halfway between Australia and Sri Lanka.
By heading for the Cocos Islands, the asylum seekers are forcing Australia's coast guard to sail thousands of miles more a month to fulfill duties to patrol Australian waters but also to help people in danger on the high seas.
More than 4,000 people have risked a boat journey to Australia this year -- almost the same number as for all of last year, The Age said.
The first of the 270-ton Armidale boats built by Austal Ships, The Armidale, was commissioned in 2005, and the last of the 14 vessels was built in 2007.
All the ships are named after cities and towns with close links to naval history. Armidale is a city in New South Wales.
The ships have twin MTU 2,320 kW diesels for a maximum speed of 25 knots and a range of around 3,000 nautical miles at an average of 12 knots.
Armaments include a Rafael Typhoon stabilized gun mount fitted with a 25mm M242 Bushmaster auto-cannon.
Warfare and decoy systems include Prism III radar warning, Toplite electro-optical detection and a Warlock direction finder.
The ships are the replacement vessels for the 15 Freemantle-class patrol boats and are the result of an aborted cooperative agreement with Malaysia signed in 1993, navy documents show.
The Offshore patrol Combatant/Joint Patrol Vessel project was abandoned in 1999 because of what would have been unacceptably high maintenance costs, the Australian navy said.
Project SEA 1444 was the new design under a "private financing initiative" deal signed with Defense Maritime Services signed in 2003.
Under the contract, Austal Ships was to build the ships and DMS would maintain them for the expected 15-year lifespan of each vessel, with the navy paying regular fees for use of the vessels.
Austal, whose head office is in Henderson, Western Australia, listed on the Australian Stock Exchange in December 1998 and since has diversified through acquisitions.
Companies bought include Western Australian shipbuilding companies Image Marine and Oceanfast as well as Canberra-based Australian Technology Information.
Austal set up a manufacturing base in Mobile, Alabama, in late 1999.
This week Austal announced the appointment of retired Rear Adm. Davyd Thomas as vice president for defense.
Thomas, who was deputy chief of the navy between June 2008 and February 2011, is based in Austal's Canberra office and is working across all of Austal's defense businesses including ships, electronic systems and in-service support.
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