An Australian man was shot in the leg during a deadly Israeli raid on a Gaza-bound aid ship in the Mediterranean, Foreign Minister Stephen Smith has confirmed.

Mr Smith said two other Australians known to be aboard the ship - a journalist and photographer - were safe after the "terrible and shocking incident", which left nine people dead.

He said the wounded Australian had received hospital treatment and been provided with consular assistance following the shooting.

The Turkish vessel was leading a convoy of six ships, with 600 people on board, and set sail for Gaza from international waters off Cyprus on Sunday in defiance of an Israeli-led blockade of the territory.

Israeli commandos backed up by warships and helicopters boarded the ships during a night-time operation in international waters.

At least nine pro-Palestinian activists were killed but Israel says its forces only opened fire after coming under attack from activists armed with clubs and knives.

Aerial footage released by Israel appears to show commandos being attacked as they abseil onto the deck of the ship.

But reports from on board the ship say the Israeli soldiers began firing first and that activists were waving white flags.

Mr Smith said he had no information of any other Australians wounded or held, but his department was seeking consular access.

"We are, through our officials, strenuously trying to ascertain the whereabouts and welfare of any other Australians," he said.

"We do know in the case of the two journalists that they are safe. So far as the injured Australian is concerned, he is being provided with consular assistance."

He said the journalists had been advised they were open for deportation.

Mr Smith said the Government would consider very carefully the best way of handling the incident, but stressed the onus was on Israel to provide a detailed explanation of the attack.

"I think we do need to proceed very calmly; there is always claim and counter-claim," he said.

"Firstly I think it is appropriate for Australians to deplore the violence and deplore the deaths.

"Certainly Australia thinks there has to be a credible investigation. The onus is on Israel to effect a credible investigation.

"The onus is on Israel to present to the international community, and in our view the [UN] Security Council, a credible, transparent investigation to these matters.

"There are of course concerns, not just expressed in Australia but throughout the international community, of the use of force and the possible use of disproportionate force."

Asked whether the incident would have a marked effect on Israel's standing in the international community, Mr Smith said:"That will depend on the way in which Israel conducts itself now."

Israel's ambassador to Australia, Yuval Rotem, accused the activists of trying to incite a confrontation to garner media attention.

He expressed sorrow over the incident, but insisted Israel had acted in self-defence.

"Israel is a democratic country and Israel has a commitment to protect its own people," he said.

"Israel cannot compromise its own security by having unchecked boats and ships going into Gaza, because these ships may carry, as far as we know, weapons that may ultimately be used against Israel."

Greens leader Bob Brown has condemned Israel's actions.

"It's a horrifying situation," he told the ABC's NewsRadio.

"The death toll has to be condemned - there is no apparent excuse [for the violence]. The Israeli government has an answer to give to the world here, and it has not given a satisfactory answer."