The confrontation was the latest sign reconciliation efforts are in trouble.
The Islamic militant group Hamas seized the Gaza Strip in 2007, leaving Abbas only with parts of the West Bank. Last week, Abbas formed a technocrat government backed by Hamas and his Fatah movement. The new Cabinet is to administer both Palestinian territories and is meant to end a seven-year territorial and political split.
However, tensions have escalated, with key disputes unresolved.
In Gaza, Hamas remains the de facto power on the ground, and for the past week has forced banks to remain closed amid a dispute with Abbas over salaries for its loyalists.
More than 40,000 employees worked for the outgoing Hamas government in Gaza, and it's not clear if they will retain their jobs or who will pay them in the meantime.
Meanwhile, Abbas has said he will continue security coordination with Israeli forces in the West Bank despite his new alliance with Hamas. The target of such joint security efforts in the past has mostly been Hamas, with Palestinian security forces loyal to Abbas clamping down on the movement.
Late Monday, Hamas supporters drove in the West Bank city of Ramallah in a convoy of about 30 cars, chanting slogans against Israel and showing support for Palestinian prisoners held by Israel.
Police broke up a Hamas rally in the West Bank late on Monday. Hassan Yousef, a Hamas leader, says officers stopped a convoy of 30 cars, seized Hamas banners and beat him and other protesters, as well as journalists.
Security agents told the protesters they would not be allowed to raise Hamas flags in public, Yousef said. "This is a very bad sign for the future of the reconciliation," he said.
Yousef Shayeb, a reporter for the local Al-Ayyam daily, said security forces ordered him to delete pictures of the protest from his mobile phone.
"When I protested, they pushed me to the ground and one of them kicked me," he said.
Adnan Damiri, the spokesman of the West Bank security forces, was not immediately available for comment.