Austin said troops sent to Iraq were not informed of what had happened to the Afghan soldiers as that would only have raised their stress levels.

"We were in a position where all we would have been able to tell them was that there had been a problem," Austin told reporters after a newspaper reported the anthrax story.

"We had not been able to identify a cause from that and we had absolutely no evidence to suggest that we were likely to see that again, based on overseas experience and our own experience when we reinstituted the program in Iraq," he said.

"So, I think to have advised people of that would have been quite counterproductive. I think that would have increased anxiety levels among our people."

At the time of the deployment to Iraq, Defense Minister Robert Hill said the anthrax shots, which were compulsory for the 2,000 military personnel sent, were safe and had anthrax shots himself to show he had confidence in the vaccinations.

Around 40 Australian troops sent to the Middle East refused to have the shots and were sent home. Many were not told of the anthrax shots until they were sailing to the Gulf.

At the time Britain allowed its troops to go to the Gulf without the anthrax shots as long as they signed a legal waiver.

The Australian newspaper reported on Saturday that defense officials were concerned about the shots as early as November 2001, citing defense documents received under freedom of information laws.

The newspaper said the program was halted for two months after 75 percent of the 1,500 Afghan deployment, including elite special forces who were to engage in fierce fighting with the Taliban, fell ill.

It said a doctor's briefing note to the then chief of the Australian Defense Force, Admiral Chris Barrie, said the side effects "could be operationally significant if the units concerned received their vaccinations after being deployed." "As a consequence of that concern, we did suspend the use of the vaccine for a period of two months but once we had been able to find that the vaccine was in fact pure and effective...we were able to reinstitute the vaccination program...," Austin said.

Austin said the side effects included increased pain and swelling in the affected arm, tiredness and lethargy, adding that in almost all cases the symptoms cleared within 48 hours and troops were able to resume normal duties.

He said the Defense Ministry did not know why the troops suffered such side effects, saying that external factors such as the hot climate and the heavy workload might have contributed.

Austin said he wanted to reassure defense personnel vaccinated and their families that they were safe.

"I do want to reassure them that we do not do these things lightly and we believe, based on good, solid scientific evidence, that the program was safe and effective," he said.