The three are the head of the Islamic Movement's northern branch, Sheikh Raed Salah, head of its southern branch, Hamad Abu Daa'bas, and Mohammad Zeidan, chairman of the Arab Higher Monitoring Committee.
Arab MK Hanin Zoabi (Balad) was released, and announced that she would convene a press conference Tuesday afternoon.
Of all 679 passengers on the flotilla, 45 were deported from Israel by plane Tuesday morning. Three additional people await flights at Ben Gurion International Airport.
An additional 130 people are expected to arrive shortly at Ela Prison in Beersheba, where they will join the 480 detainees imprisoned there.
The Israel Prison Service says the prisoners will not be brought before a court because they are imprisoned under special orders by the Interior Ministry, however they are allowed to meet with attorneys or consuls from their home country if they wish.
Each prisoner, upon arriving at the prison, received a package including underwear, blankets, a towel, toiletries, and more. They were fed and then placed in their cells to sleep.
Israeli-Arab passengers of the flotilla were not taken to Ela, but rather transferred to the police. It is unclear as yet what awaits the foreigners, whether deportation or criminal charges of some sort.
Meanwhile the bodies of nine people killed on board the Marmara have been transferred to the Abu Kabir Forensic Institute, where officials await orders from the police.
The Immigration Authority says there were 679 people in all aboard the flotilla's boats, most of them Turkish and Greek. Citizens of Serbia, Oman, Pakistan, Malaysia, Macedonia, Yemen, Kosovo, and Bahrain were also on board.
Police are also slated to request an extension of the remand of 18 youths arrested on Monday for rioting in Umm al-Fahm, Nazareth, Fureidis and Haifa.
A police statement said, "We will continue with a firm policy against anyone who uses any kind of violence. We will allow protests, but not riots."
Meanwhile, thousands of Northern District Police officers are preparing for possible scenarios. Northern District Police Chief Shimon Koren is holding talks with leaders of the Arab public in hopes of maintaining calm and restraint.
Shmulik Hadad contibuted to this report