General Cosgrove said the ADF's approach to the matter had been entirely reasonable and had aimed to protect personnel against biological threats.

"Now I'm delighted to see that those threats didn't eventuate, but at the outset we didn't know that," he said.

"Accordingly, it was the only responsible decision.

"There's no penalty on those young people.

"They're back to work now wherever they are."

The issue became public in February when several sailors were flown off the HMAS Kanimbla after discovering en route to the Gulf they had to be inoculated against the deadly disease.

General Cosgrove said any claims of harassment were being looked at.

"If there is one or two claims from individuals that they've been harassed, that's being investigated," he said.

General Cosgrove said all ADF personnel were given a choice on whether or not to accept unusual vaccinations like anthrax.

"They're continuing in their jobs now. They had the choice. They exercised the choice. We respected their decision and we brought them home without penalty," he said.

Opposition defence spokesman Chris Evans said yesterday while 52 personnel were flown home many more were forced into having the vaccine.

Senator Evans said the Government had covered up the matter and he hoped a defence inquiry into the vaccinations would reveal the real story.