Israel is facing a backlash from the international community after a deadly raid on a Gaza-bound aid flotilla claimed the lives of nine people on Monday morning.

Many of those killed are believed to be Turks, and Turkey has recalled its ambassador from Israel -- a huge blow to diplomatic relations between the two countries.

Six ships were part of the flotilla headed to Gaza, intending to bring in 10,000 tons of aid and some 700 activists -- the majority of whom were riding on a Turkish-flagged ship called the Mavi Marmara.

The ships were ordered to stop their journey into Gaza -- which is under an Israeli blockade -- before they were raided by Israeli forces. They were in international waters, about 130 kilometres from the Gaza coast, when the raid began in the early hours of Monday morning.

Israeli commandos rappelled from helicopters down onto the top of the Mavi Marmara, where the violence occurred, said Israeli military chief Gabi Ashkenazi.

Conflicting reports of what happened emerged from the military and the activists riding in the flotilla.

The Israeli government said that when commandos landed on the ships, they were attacked with sticks, knives and hit with gunfire. Israeli Prime Minister Benjamin Netanyahu said the soldiers had no choice but to defend themselves.

"They had to defend themselves, defend their lives, or they would have been killed," he said.

The army said five soldiers were injured in the raid, including two who were shot with pistols seized from Israeli forces. The Israeli military released a video of the incident that appeared to show activists striking soldiers with clubs, and throwing one person overboard.

But an Al-Jazeera reporter said Israel fired upon one of the ships before boarding, and that the ship's captain was wounded.

Adam Shapiro, a member of the Free Gaza movement, a Pro-Palestinian group that helped organize the flotilla, said the Israeli military video may have started after soldiers opened fire. Organizers of the flotilla also had a live feed broadcasted online.

"The Israelis have not indicated at what point in time they are showing their soldiers being hit. We know from our own live feed … that the initial soldiers who came aboard the ship opened fire immediately upon coming on the ship, and by the time anybody picked up a club there was already one dead, many injured."

He also said activists aboard the ships had only been trained in non-violent resistance.

"We have to prepare them to face Israeli soldiers who will use violence against them," he said.

The raid brought swift condemnation from many members of the international community and UN Secretary-General Ban Ki-moon who called for a "thorough" investigation and explanation from Israel.

Robert Serry and Filippo Grandi, two senior United Nations officials involved in the Middle East peace process, issued a joint statement condemning Israel's action.

"We wish to make clear that such tragedies are entirely avoidable if Israel heeds the repeated calls of the international community to end its counterproductive and unacceptable blockade of Gaza," they said.

Meanwhile, Netanyahu cut short a trip to Canada and cancelled a planned meeting with U.S. President Barack Obama, so that he could fly home to Israel.

Activists were warned: spokesperson

Mark Regev, a spokesperson for Israeli Prime Minister Benjamin Netanyahu, said the flotilla had been warned in advance that the ships would not be allowed to enter Gaza from the sea.

"Unfortunately these people wanted a confrontation and they charged our blockade," Regev told Canada AM from Jerusalem on Monday morning.

Israel has had a blockade in place for the past three years, ever since the coastal territory was seized by Hamas.

Israel has let five aid deliveries go through the blockade on previous occasions, but has blocked all such attempts since January of last year.

Regev said the Israeli government had offered to inspect the aid shipments, before allowing them through to Gaza where about 1.5 million people live. A similar offer was made by the Egyptian government, but was not accepted by the people on board the boats.

Regev said the commandos were under strict instructions to use minimal force. But when they came under attack, they were forced to respond.

"Unfortunately, the minute they came on the ship, they were attacked by very deadly force – knives, iron bars and of course, live fire. And the violence was initiated by the people on the boat," said Regev.

"And of course, all violence is regrettable and anyone killed is regrettable, but it's clear which side initiated the violence."

Canadian on board flotilla ship

Berlin said a Canadian, Kevin Neish of Victoria, B.C., is on one of the ships in the flotilla. However she said as far as she knows, Neish was not on a ship where casualties occurred.

"There were six ships. We have a boat called the Challenger I, which is flagged in the United States. He was on that boat and as far as I know he hadn't transferred over to the Turkish ship," Berlin said.

However, in other reports Neish is said to be on a ship called the Challenger II. It is unclear whether they are the same ship. Neish is reportedly tasked with protecting a team of news reporters travelling with the flotilla.

The incident Monday brought scorn from Gaza's Hamas government and Palestinian President Mahmoud Abbas. The United Nations and other countries demanded an explanation from the Jerusalem government.

"We are in contact with the Israeli authorities to express our deep concern and to seek a full explanation," said Robert Serry, the highest-ranking UN official in the region.

Following the altercation, the Israeli military shut down all satellite phones on board the ships and a group of embedded reporters were unable to communicate from the scene.

After the raid, the Israeli military started towing the ships back to the Israeli port of Ashdod. Five had reached the port by early nightfall.

Police spokesperson Micky Rosenfeld said 16 people were arrested after refusing to identify themselves.

With files from The Associated Press and The Canadian Press