The number of people killed between the start of the Al-Aqsa Intifada (uprising) on 28 September, 2000 and 31 July 31, 2003 stands at 2647 of which 1157 were from the Gaza Strip and 1490 from the West Bank, it said in a statement.
Of that number, 482 victims were children and 178 women.
The figures include Palestinians killed in attacks and those assassinated by the Israelis.
During the 34-month conflict, 36,448 people were wounded, 11,390 in Gaza and 25,058 in the West Bank, the statement said.
"The Palestinian Authority should not take on the role of the occupier"
The report also put the total number of Palestinians in Israeli jails at 7389 up to the end of July.
Since the figures were compiled, Israel has released around 400 Palestinian prisoners.
Meanwhile, Palestinian security services on Wednesday arrested two men on suspicion of setting off a bicycle bomb outside the Palestinian internal security HQ here last week, an interior ministry source said.
The source, on condition of anonymity, said security forces went to Gaza City's Shati refugee camp to arrest Izmeh Ala Erkalan, suspected of sending the explosives-laden bicycle which blew up without causing injury.
When Erkalan spotted the security forces, he and another man opened fire, provoking a gunfight, during which the suspect was shot in the leg. Both gunmen were detained for questioning on criminal charges, the source said.
Islamic Jihad leader Muhammad al-Hindi said Erkalan was a member of the group's armed wing, Al-Quds Brigade, and said contact was made with the Palestinian Authority "to calm the situation".
Al-Quds Brigade issued a statement condemning the arrest of two of its members, one of them a local leader of the group, and calling for their immediate release.
"The Palestinian Authority should release our fighters today or they will be responsible for the consequences," the group said, warning Palestinian security forces "not to take on the role of the (Israeli) occupiers".