The signatories, in a message to Arafat and the Fatah Central Committee, condemned the "dramatic situation" within the movement which had failed to respond to calls for reforms.
The nationalist movement was formed in 1959 by Palestinian exiles living at the time in Kuwait, but Palestinians generally consider its birth to be 1 January 1965, the date of the first Fatah attack in Israel.
The turmoil in Fatah coincided with more violence in the Gaza Strip, where Israeli troops shot dead a Palestinian late on Saturday.
An Israeli army spokeswoman said the Palestinian was killed as he tried to approach the fence of a Jewish settlement in the southern Gaza Strip.
"Two figures were seen stealing towards the security fence in an area off-limits to Palestinians. The force opened fire and identified having hit both of them," she said, adding that only one body had been found by the army.
Palestinian witnesses confirmed seeing one person shot down just outside the security fence surrounding the Gush Katif settlement block.
The latest death brought to 3741 the number of people killed since the outbreak of the Palestinian intifada or uprising in September 2000. It included 2798 Palestinians and 878 Israelis.