Israeli Prime Minister Benjamin Netanyahu is defending Israeli commandos who launched a deadly raid on a flotilla of humanitarian ships destined for Gaza, saying they acted in self-defence.

Nine people were killed and dozens were wounded in Monday's pre-dawn raid, which happened in international waters more than 60 kilometres from shore.

Netanyahu said the Israeli soldiers had boarded one of six ships in the flotilla at about 4 a.m. local time to check it for weapons when they were attacked by activists with knives and clubs.

Night-vision footage released by the military showed soldiers dropping from a helicopter one by one and being grabbed by a mob of men wielding sticks on the lead boat, the Turkish-flagged Mavi Marmara.

The soldiers succumbed to the assailants and fell to the deck, where the men continued to beat them and dump one of them from the top deck.

"They literally attacked the first soldiers on the ship, they were mobbed," Netanyahu said in Ottawa, where he was meeting with Prime Minister Stephen Harper. "They were clubbed, they were beaten, stabbed, there was even a report of gunfire.

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

Israeli officials say at least five Israeli soldiers were wounded in the confrontation.

Meanwhile, the UN Security Council was holding an emergency meeting on the situation Monday afternoon.

Assistant Secretary-General Oscar Fernandez-Taranco said in his briefing to the UN's most powerful body that Monday's bloodshed would have been avoided "if repeated calls on Israel to end the counterproductive and unacceptable blockade of Gaza had been heeded."

Turkey's Foreign Minister Ahmet Davutoglu called the raid "murder conducted by a state" and demanded an immediate Israeli apology, an urgent inquiry, international legal action against the authorities and perpetrators responsible, and an end to the Gaza blockade."

Netanyahu, who began a two-day official visit to Canada on Sunday, cut short his visit and was expected to leave Ottawa for Israel Monday afternoon.

He also rescheduled a Tuesday meeting with U.S. President Barack Obama in Washington, officials said.

Israeli Prime Minister Benjamin Netanyahu makes brief comments following his meeting with Canadian Prime Minister Stephen Harper following their meeting on Parliament Hill on Monday. (Adrian Wyld/Canadian Press)

Palestinian President Mahmoud Abbas condemned the Israeli "aggression" and declared three days of mourning across the West Bank. He called on the United Nations Security Council and Arab League to hold emergency sessions on the incident.

Israeli Deputy Foreign Affairs Minister Danny Ayalon said Israel regrets the loss of life but called the moves from the flotilla "premeditated" and an "outrageous provocation."

"The organizers are well known for their ties to global jihad, al-Qaeda and Hamas," he said. "On board the ship, we found weapons prepared in advance and used against our forces."

Communications to the ships were cut shortly after the raid began, and activists were kept away from reporters after their boats were towed to the Israeli port of Ashdod.

Helicopters evacuated the wounded to Israeli hospitals, officials said. Five ships had reached port by early evening, and some 136 activists had been removed without serious incident, the military said.

Sixteen were jailed for refusing to identify themselves, police spokesman Micky Rosenfeld said. Israel had said activists would be given the choice to be deported or imprisoned.

No provocation: Free Gaza Movement

The aid convoy was organized in part by the Free Gaza Movement, an international group of pro-Palestinian activists that claims the Gaza blockade is a violation of international law.

Israeli naval vessels approach the port of Ashdod on Monday after commandos stormed Gaza-bound aid ships. (Nir Elias/Reuters)

Audrey Bomse, the legal co-ordinator for the Free Gaza Movement, called claims the passengers had planned to provoke the soldiers "absurd."

"It was clearly an attack — probably a premeditated attack — by Israel upon civilians," she told CBC News.

"These are supposed to be crack military forces. I can only assume that they wanted to intimidate people from doing this in the future."

Ghassan Khatib, a Palestinian government spokesman, said the government "condemns the brutality in which the Israeli government treated this peaceful attempt to break the siege on Gaza."

The Palestinians were calling on the international community to pressure Israel to end the three-year blockade of the territory, he said.

Ayalon said Israel offered to deliver the aid supplies through the "appropriate" channels, and did "everything" it could to avoid a violent outcome.

Israeli naval ships escorted the flotilla to the port of Ashdod, where officials were trying to identify the ships' passengers.

International reaction

"Canada deeply regrets this action, the loss of life and the injuries that have occurred and obviously we'll be looking in the days that follow to get all the information we can get to find out exactly what has transpired," Harper said following a meeting with Netanyahu.

Protesters in Lahore, Pakistan, rally to condemn Israel's assault on a flotilla of ships carrying aid and pro-Palestinian activists to the Gaza Strip on Monday. (K.M. Chaudary/Associated Press) Speaking with Netanyahu by phone, Obama expressed "deep regret at the loss of life in today's incident and concern for the wounded," according to a White House statement. He also expressed "the importance of learning all the facts and circumstances" surrounding the event, it said.

Elsewhere, the raid drew swift condemnation.

Turkey, usually an Israeli ally, recalled its ambassador to Israel and said it would cancel several military drills with Israel. The Turkish deputy prime minister also called on the UN Security Council to convene an emergency session.

UN officials and the European Union's foreign affairs chief, Catherine Ashton, called on Israel to carry out an inquiry.

Israeli ambassadors in Sweden, Spain, Denmark and Greece were summoned for meetings.

Protesters took to the streets around the world, including England, Iran, France, Pakistan and Italy, burning flags to show their anger at the raids.

With files from The Associated Press and The Canadian Press