"There are 21 passengers detained who refused to be expelled immediately and are engaged in proceedings against their deportation before an Israeli judge," interior ministry spokeswoman Sabine Haddad told AFP.
"Only after these proceedings are complete... can they be deported," she said.
The 21 activists were among 27 passengers and crew aboard two ships intercepted by the Israeli navy as they tried to run the blockade of the Gaza Strip.
Israeli commandos boarded the Irish-flagged Saoirse (Freedom) and the Canadian ship Tahrir (Liberation) in international waters off Gaza on Friday before the navy escorted them to the port of Ashdod, the Israeli military said.
On Saturday, Israel freed six of the passengers -- an Arab-Israeli, two Greek crewmen, and three journalists from Egypt, Spain and the United States.
She said the remaining 21 people were still being held at a detention facility in Ramla near Tel Aviv, after questioning by immigration authorities.
Those still in Israeli detention are from Australia, Britain, Canada, Ireland and the United States.
The attempt to sail to Gaza was the latest in a string of activist missions aimed at breaching Israel`s blockade of the territory.
In May 2010, six ships led by the Turkish Mavi Marmara tried to reach the coastal strip, but were intercepted by Israeli commandos, who stormed the boats, killing nine Turkish activists and sparking a diplomatic crisis with Ankara.
Earlier this year, a second flotilla tried to reach Gaza, but several ships were sabotaged -- which activists blamed on Israel -- and the one boat that made the sailing was intercepted before it could reach Gaza.
Israel says its blockade is necessary to prevent weapons from entering the coastal territory, which is run by the Islamist Hamas movement.
Two months ago, a UN report on the 2010 flotilla raid accused the Jewish state of acting with "excessive force" but found that its naval blockade of Gaza was legal. (*)
Editor: Kunto Wibisono
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