Natural Resources Minister Gary Lunn may have known in September that the Chalk River reactor needed improvements to protect public safety, months before it was shut down, according to an auditor general report released Tuesday.

Auditor general Sheila Fraser said she presented a report on Atomic Energy of Canada Ltd. (AECL) to the corporation's board on Sept. 5, 2007.

The cover page of the audit says: "We would like to draw your attention to a significant deficiency related to the unresolved strategic challenges that the Corporation faces ... it is our view that this report contains information that should be brought to the attention of the Minister of Natural Resources. Accordingly, following consultation with the Board, we will be forwarding a copy of the report to the Minister."

The report goes on to highlight "three strategic challenges" AECL faced, including "the replacement of aging facilities at Chalk River Laboratories (CRL)."

Liberal MP Omar Alghabra, the natural resources critic, had asked Fraser's office to audit AECL. He has suggested Lunn was slow to take action on the aging Chalk River reactor.

"We have reports -- and the minister has yet to answer these questions -- that he may have known about this way before December third," Alghabra told CTV's Mike Duffy Live before the audit was released. "If he knew on Nov. 22 or even sooner, why didn't he act sooner?"

Earlier Wednesday, oposition leaders called for the resignation of Lunn, following accusations that he improperly interfered with an arm's-length nuclear regulator.

Lunn is currently engaged in a very public dispute with Linda Keen, the president of the Canadian Nuclear Safety Commission (CNSC), over the shut down of the Chalk River nuclear reactor in Ontario late last year.

"We believe that the minister should be fired, the prime minister should apologize for having put into question the neutrality of a senior official," Liberal Leader Stephane Dion told reporters Wednesday.

The CNSC is responsible for setting licensing, health and safety rules for the country's nuclear facilities.

In a letter dated Dec. 27, Lunn threatened to fire Keen for her involvement in keeping the reactor closed.

"These events have cast doubt on whether you possess the fundamental good judgment required by the incumbent of the office of President of the Commission, and whether you are duly executing the requirements of the office," wrote Lunn.

He ended the letter by saying he was considering making a recommendation that Keen's "designation as President of the Commission be terminated."

On the CNSC website, Keen has posted both Lunn's letter and her response -- in which she says:

"The nature of the allegations which have been made, coupled with your threat to have me removed as President, seriously undermine the independence of the CNSC."

The Liberals want Lunn to appear before the Natural Resources committee to explain his actions regarding the Chalk River isotope crisis. They also want Keen to appear.

On Wednesday, the Green Party of Canada called for Lunn's resignation for his "interference with and threats to the independent nuclear regulator."

"Minister Lunn's threats... cross the line of appropriate political deference to an independent regulator. Such directives and threats weaken the credibility of nuclear safety in Canada," Green Party leader Elizabeth May said in a press release.

The Green Party wants a full inquiry into the nuclear industry.

On Tuesday, the NDP called on the government to create a special committee to investigate what went wrong.

"Instead of making allegations, the Minister should ask his colleagues to get to work and fix the government appointment process, something Harper promised to do," said NDP critic for government operations Charlie Angus.

"The Commissioner is an independent watch dog and should not be taking the fall for the Minister's incompetence. The Minister should have systems in place to ensure that things like this don't happen."

Chalk River problems

The Chalk River reactor stopped production for scheduled repairs on Nov. 18 and was expected to restart within five days.

But the CNSC refused to allow the reactor to restart after finding it had been operating without a backup emergency power system for cooling pumps for 17 months.

The reactor produces radioactive substances used in diagnostic tests for cancer, heart problems, and bone ailments. It provides enough medical isotopes for about 25 millions tests and treatments each year.

As a result of the extended closure, an international shortage of the substance occurred and thousands of tests were delayed and/or cancelled.

"What was going on was a major international health crisis, because of essentially an argument between two agencies over paperwork," said Conservative MP Jason Kenney.

"The issue was not really substantially about safety, it was about licensing, about one part in a back-up system that would only be relevant in a once-in-50,000-years seismic event."

In December, emergency legislation passed by Parliament side-stepped the CNSC's objections and allowed the Atomic Energy of Canada Ltd. to restart the reactor for 120 days in order to alleviate the isotope shortage.

Judy Wasylycia-Leis, the NDP health critic, said the government should have been aware of the reactor's problems long before the situation escalated.

"Issues around Chalk River have been raised time and time again -- issues about safety," she said. "The Conservative government chose to ignore the problems and to wait until a crisis loomed before the Canadian population."

With files from CTV's David Akin and The Canadian Press