They said the gunmen opened fire as about 200 Hamas activists and armed men were preparing for a rally in the city of Nablus. There was no immediate comment from Fatah.
Violence between the rival factions has erupted since Abbas called for early elections a week ago. The two sides agreed on a ceasefire in Gaza earlier this week following days of fighting that killed 10 people in the strip.
The Islamic group Hamas, which is sworn to Israel's destruction, defeated Abbas's long-dominant Fatah party in elections in January.
Hamas has rejected Abbas's call for fresh parliamentary and presidential elections and said such a move amounts to a ''coup''.
Unknown gunmen clashed with Hamas fighters near the Gaza City home of the Hamas-led government's Foreign Minister Mahmoud al-Zahar early today, Palestinian witnesses said.
Local residents said they suspected the gunmen were from a local clan rather than Fatah. No casualties were reported.
Abbas made his election call after talks on forming a unity between Fatah and Hamas collapsed. The aim had been to establish a cabinet that could end Western isolation of the government.