Dozens of  activists seized in the deadly raid on a Gaza-bound aid flotilla arrived in Jordan on Wednesday after being deported from Israel, according to Jordanian officials.

The 124 activists from 12 Muslim nations — most of them without diplomatic ties with Israel — crossed the Allenby Bridge aboard five Jordanian buses.

The group included 30 Jordanians, 16 Kuwaitis and activists from Azerbaijan, Indonesia, Malaysia, Pakistan, Algeria, Morocco, Mauritania, Yemen, Oman and Bahrain.

Dozens of other activists remain in Israeli detention, but most are expected to be deported in the coming days.

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An activist arrested aboard a Gaza-bound ship looks out the window of a bus upon arrival to Ella prison in the southern Israeli city of Beersheba on Tuesday. ((Herzl Yosef/Reuters))

Earlier Tuesday, Yigal Palmor, a spokesman for Israel's Foreign Affairs Ministry, told CBC News there was no one left on the ships and that passengers who identified themselves were taken to the airport, while the others were detained.

The ships tried to break the three-year blockage of Gaza to deliver humanitarian aid when they were raided by Israeli commandos early Monday.

Turkish woman Nilufer Cetin said she agreed to leave Israel after being warned jail conditions in Beersheba would be "too harsh" for her one-year-old, whom she'd brought on the voyage.

Canada's Foreign Affairs Ministry confirmed three Canadians had been detained, but would not elaborate.

"We are working with local authorities and are providing consular assistance as required. Due to the Privacy Act, no further information can be released," ministry spokesperson Ambra Dickie wrote in an email to CBC News.

Kevin Neish, 53, a retired engineer and activist from Victoria, is believed to be among those in confinement. His daughter Jennifer said Tuesday that she'd received confirmation from Canadian government officials that her father was alive and well and would be deported from Israel within 72 hours.

His brother, Steve Neish, said Tuesday morning it was unlikely his brother had been injured in Monday's attack and that he was sure "his overall safety is OK."

"He's fully aware of the dangers [of such missions]," Steve Neish told CBC News. "It's a bit unpredictable though, so you don't know, you're never sure what is going to happen."

"No one was expecting bullets," said Neish's friend, Zoe Blunt.

"He was expecting to take a beating at the hands of the Israeli army. He was not expecting anyone to get shot."

Activists describe raid

Turkey said Tuesday it was sending three ambulance planes to Israel to pick up 20 more Turkish activists injured in the operation.

Three Turkish Airlines planes were on standby waiting to fly back other activists, the prime minister's office said.

Five Germans, six Greeks and several others were released, but Israel barred access to hundreds of other activists seized during the raid Monday that killed at least nine people and wounded dozens.

One of the Greeks, who had been a crew member, told reporters that Israeli commandos boarded the boats in international waters about 130-145 kilometres off the Israeli coast.

The Greeks told reporters the Israelis beat activists with clubs and used electric shocks, and said they heard shooting aboard the Turkish boat, the Mavi Marmara, ahead of theirs.

The Israeli government says its soldiers were defending themselves, and has released video showing soldiers in riot gear being struck by activists with sticks. One soldier appears to have been shoved into the water.

Israel says the activists were armed with metal rods, knives, slingshots and two pistols snatched from the troops.

When asked about the Israeli video, Norman Paech, a former member of Germany's Left Party who was aboard the Marmara, said he only saw three activists resisting.

"They had no knives, no axes, only sticks that they used to defend themselves," Paech said at a news conference in Berlin, after he returned from Tel Aviv.

Still, he said, he could "not rule out" that others used weapons somewhere else on the boat.

Some 400 Turkish activists were part of the flotilla, along with more than 30 Greeks and people of some 20 other nations including Canada, Germany, the U.S. and Russia.

With files from The Associated Press and The Canadian Press