South Africa will recall for consultations its ambassador to Israel following a deadly attack on a vessel attempting to deliver humanitarian aid to Gaza, Deputy International Relations Minister Ebrahim Ebrahim said on Thursday.

However, government had no intention of expelling the Israeli ambassador to South Africa or of cutting diplomatic ties with that community.

"The recall of ambassador Ishmael Coovadia for consultations is a way of protesting and a way of showing our strongest condemnation of the attack.

"This recent Israel aggression of attacking the aid flotilla severely impacts on finding a lasting solution to the problems of the region," Ebrahim told journalists in Pretoria.

He could not say when Coovadia would return to Israel.

Nine people were killed during Monday's raid in international waters, an act that Ebrahim called "unacceptable". The vessel involved in the incident was part of a flotilla trying to break Israel's blockade on Gaza and deliver aid to the area.

Israel had since started releasing and deporting those activists who were arrested during the military attack, including a Cape Town based journalist, Gadija Davids.

Davids was flown out of Israel with others on Wednesday night by the Turkish government.

She was currently in Istanbul with South Africa's ambassador and would be arriving home on Friday, said Ebrahim.

South Africa had already added its voice to the increasing international condemnation of Israel's actions and had summoned the Israeli ambassador to a meeting.

This was the second time in 15 years that South Africa had recalled an ambassador in a foreign country.

In 1995, former President Nelson Mandela recalled then High Commissioner George Nene from Nigeria when the country executed the leader of the Movement for the Survival of the Ogoni People, Ken Saro-Wiwa and eight others. The execution was carried out despite appeals for clemency by various governments, including South Africa.

Ebrahim said that there had been no discussion about closing down the two embassies in Israel - one in Ramal and the other in Tel Aviv - as these were important for monitoring purposes.

"It could contribute to resolving some problems in the region," he said.

Government had also joined the international community in its call for the siege of Gaza to be immediately lifted.

"This siege, which has brought untold hardships to the ordinary people of Gaza and made their lives nightmarish, is unconscionable and unsustainable," said Ebrahim.

Acknowledging demonstrations that had been taking place in many cities against this incident, Ebrahim assured the public that government would continue to do whatever was possible.

He also spoke of government's commitment to contributing towards finding peace in the region and ensuring an independent and viable Palestinian state, as agreed to by all parties.

"A long term solution to the region can only be achieved through negotiation. What is needed is the creation of a climate of mutual trust and peace."

Ebrahim welcomed the decision by Egypt to open the border crossing between it and Palestinian-controlled Rafah.