The gunmen, angry over Fatah's stunning election loss this week to the militant group Hamas, chanted that Fatah will not participate in a Hamas-led government.
Some gunmen later approached the compound of Palestinian Authority President Mahmoud Abbas. There were no reports of casualties.
Meanwhile, the senior leader of Hamas says the group will not disarm or change its policies toward Israel. Speaking Saturday from his base in Damascus, Syria, Khaled Mashaal also said the Palestinians will not be blackmailed by international threats to cut off Palestinian aid.
Hamas has claimed many suicide attacks against Israel in recent years and has vowed to destroy the Jewish state.Some information for this report was provided by AFP, AP and Reuters.