Earlier three air ambulances landed at a military base in Ankara, the Turkish capital, carrying wounded activists who were transferred to hospitals in the city.
Hundreds of supporters including Bulent Arinc, Turkey's deputy prime minister, and several other Turkish politicians were at the airport in Istanbul to welcome the returning activists.
"They faced barbarism and oppression but returned with pride," Arinc told hundreds of jubilant relatives and supporters outside the airport, chanting "God is Great!"
A crowd of several thousand also gathered in central Istanbul to celebrate the activists' return.
Officials in Israel said earlier that they had released about 700 activists from 42 countries that were seized from the Gaza aid flotilla.
More than 100 of the activists, mostly from Arab countries, were driven by buses across the Allenby Bridge into Jordan on Wednesday.
An aircraft carrying 31 Greek activists, together with three French nationals and an American, flew into Athens airport in the early hours of Thursday, the Israeli foreign ministry said.
Seven activists wounded in Monday's clashes were still being treated in an Israeli hospital, it said.
Three others - an Irishman and two women from Australia and Italy - remained in Israel "for technical reasons", the ministry said.
But Ayman Mohyeldin, Al Jazeera's correspondent in Jerusalem, said that four Palestinian-Israelis remain in prison.
Israel has remained defiant about the raid and says it is ready to intercept another aid ship, the Rachel Corrie, that organisers of the Freedom Flotilla say is due to head for the Gaza Strip next week.
Accusing international critics of "hypocrisy," Binyamin Netanyahu, the Israeli prime minister, defended the seizure of the aid ships on Wednesday.
"This was not a 'love boat'," Netanyahu said in a televised address to the nation, referring to the vessel boarded by commandos. "It was a hate boat."
"These weren't pacifists, these weren't peace activists, they were violent supporters of terrorism."
Netanyahu said the aim of the flotilla was to break the blockade of Gaza, not to bring aid.
He said that if the blockade ended, ships would bring in thousands of missiles from Iran to be aimed at Israel and beyond, creating what he said would be an Iranian port on the Mediterranean.
"The same countries that are criticising us today should know that they would be targeted tomorrow," Netanyahu said.
However, Ban Ki-moon, the UN secretary-general, said the flotilla tragedy only highlights the serious underlying problem - namely, the siege imposed on the Gaza.
He said that the siege was "counter-productive, unsustainable and wrong".
"It punishes innocent civilians," he said.
Ban said the siege should be lifted immediately.
No mention of inquiry
Netanyahu's comments came hours after Turkey warned it would cut off diplomatic ties with Israel if its citizens killed and injured in the Gaza flotilla raid were not returned by Wednesday night.
Our correspondent said his address did not include mention of an inquiry into the attack, as many have demanded.
"If the international community or the Turkish government were waiting to hear Binyamin Netanyahu announce an independent investigation to look into this deadly raid, it certainly did not come as expected, or as the international community and the UN Security Council had demanded," Mohyeldin said.
|Thousands of protesters welcomed the activists' return to Turkey [Reuters]
"Instead the Israeli prime minister once again defended the Israeli course of action."
On the other hand, Ahmet Davutoglu, Turkey's foreign minister, called for an international commission into the raid.
"We have clearly stated that we would review our ties with Israel if all Turks not released by the end of the day," he said on Wednesday.
Davutoglu also said Turkey was ready to normalise ties with Israel if it lifted its blockade on Gaza, saying "it was time calm replaces anger".
Relations between Turkey and Israel deteriorated rapidly following the deadly raid, with most of the bloodshed occurring on the Mavi Marmara, a Turkish-flagged ship carrying hundreds of pro-Palestinian activists.
State media reported on Wednesday that Turkey's justice ministry is considering legal action against Israel.
Officials are looking into both domestic and international law to see what action might be undertaken after Monday's operation in international waters, a report by the Anatolia news agency said.