Defence Minister Stephen Smith, clearly annoyed on Tuesday, says the ships had been treated almost as second-class vessels with systemic and cultural problems in their maintenance.
He told a conference of industry executives he was disappointed by defence's can-do-and-make-do culture.
An independent team, headed by businessman Paul Rizzo, will assess how defence could improve management of ship maintenance and repair.
Problems with the navy's landing ships emerged late in 2010 with HMAS Kanimbla and HMAS Manoora docked for unexpected maintenance.
Both are 40-year-old former US Navy vessels that Australia acquired in the mid-1990s.
The government has announced it will retire Manoora and proceed with repairs on Kanimbla for a return to service in April 2012.
Mr Smith said the advice it received from navy was a frank appraisal, identifying systemic and cultural problems in maintenance of the amphibious ship fleet for more than a decade.
"It outlines the adverse side effects of a can-do-and-make-do culture and a lack of sufficient adherence to verification, certification and assurance processes," he told the annual Australian Defence Magazine congress in Canberra.
There was a perception that major support ships were not subject to the same level of risk as submarines and aircraft.
"Almost a perception that HMAS Manoora and HMAS Kanimbla are second-tier ships," Mr Smith said, adding insufficient resources were being applied to address shortcomings.
Both vessels would have been extremely useful to assist disaster relief operations following the Queensland cyclone.
The problems with the navy's heavy-lift capability had been aggravated by the non-availability of HMAS Tobruk, also because of ongoing maintenance issues, Mr Smith said.
The Rizzo team will develop a plan to address causes of the problems facing the availability of the amphibious and support ships and oversee early implementation of reforms.
Two new large amphibious landing ships will enter service about 2015.
Until then, the government is considering various options including acquiring a surplus British landing ship.
Australia also has agreed to share use of the New Zealand navy's landing ship HMNZS Canterbury for some operations.
"The current state of our amphibious lift capability is a sobering reminder of the challenges we face and the risks that we run if defence and defence industry don't get it right," Mr Smith said.