Another 80 people were injured in a security crackdown on the rally, which had been called to mark the third anniversary of the popular Palestinian leader Yasser Arafat's death. The rally, planned as a demonstration of opposition to Hamas rule, was reported to have attracted over 250,000 people.
"The abductions and arrests of Fatah and other party members have been continuing since last night," Fahmi Al-Zaarir said. "The number of those arrested is being verified. But at least 350 people are known to have been detained."
While police officials in the Hamas-controlled Gaza Strip confirmed the arrests, they disputed the number of people detained.
"We have been conducting arrests since last night. Dozens, not hundreds, of people have been arrested," Ihab al-Hussein, a Hamas security spokesman, said.
Hamas and Fatah have blamed each other for the violence. Hamas says demonstrators were the first to open fire, while Fatah insists its people were unarmed, calling the bloodshed "a terrible crime."
Palestinian President Mahmoud Abbas declared three days of mourning on the Fatah-controlled West Bank. Flags have flown half-mast, and many stores, schools and colleges are closed. Mourning is not formerly being observed in Gaza.
Abbas has ruled out dialogue with Hamas until it gives up control of Gaza, which it seized from Fatah in June following violent clashes. Later this month, the Palestinian leader is expected to take part in a U.S.-hosted conference with Israel and other Middle East nations on Palestinian statehood.