John Kerin – John Howard has used a previously top-secret report to comprehensively reject explosive claims of intelligence agency failures by Lieutenant-Colonel Lance Collins.

The rebuff comes in a seven-page letter to Lieutenant-Colonel Collins, obtained by The Australian, in which the Prime Minister rejects the whistleblower's call for a royal commission.

But it also comes as the lawyer representing Lieutenant-Colonel Collins, David Rofe QC, accused Defence Minister Robert Hill of orchestrating a "cover-up of a cover-up" in refusing to release annexes of reports crucial to his client's claims.

In his letter, Mr Howard says he cannot share Lieutenant-Colonel Collins's judgment that there was a series of intelligence failures on East Timor militia violence, Iraq's weapons of mass destruction, the Bali bombing and a host of other incidents.

Mr Howard says intelligence forms only part of the picture that informs policy and Lieutenant-Colonel Collins could not have had access "to all the available intelligence material".

"On the basis of the advice I have received, I cannot share your overall judgment about the performance of the Australian intelligence community," Mr Howard says.

In rejecting Lieutenant-Colonel Collins's accusations that his warning of Indonesian-backed militia violence was ignored, and that a pro-Jakarta lobby existed within the Defence Intelligence Organisation, Mr Howard refers to the findings of a previously classified report carried out by the former inspector-general of intelligence and security, Bill Blick.

Mr Howard says Mr Blick was "unable to find evidence of a systemic or institutional bias in DIO reporting" in 1998-99.

"Indeed [Mr Blick] observed that the overall picture throughout the period is of conscientious (DIO) attempts to analyse what was going on," he says.

Mr Blick found that "what Colonel Collins interpreted as an attempt to quash contrary views appear to be legitimate expressions of concern about parts of the content of his assessment and about his wide distribution of assessments and comments". Mr Howard says he met Indonesian president BJ Habibie at the time and urged him to accept international peacekeepers before East Timor's independence ballot.

"Unhappily, he would not agree," he adds. "For us to have nevertheless inserted our forces without Indonesian acceptance would have amounted to an illegal invasion."

Mr Rofe told The Australian last night that the failure to release annexes to a report by Captain Martin Toohey, which backed the Collins claims about the DIO, was "nothing but a cover-up of a cover-up".

"Didn't Senator Hill say he didn't want any secrets? Then why won't he release the annexes?" Mr Rofe said.