Backed by gunmen from the Fatah party, police blocked access to the crossing with Egypt and forced EU monitors manning it to flee, the BBC said.
The Palestinian Authority took control of the crossing last month after a deal brokered by the United States. Under the terms of the agreement, EU monitors must be present for the crossing to operate. Those who fled the police surge are expected back when it's safe.
Julio de la Guardia, a spokesman for the EU monitors, said Palestinian police had advised them to leave and that they temporarily withdrawn to the Israeli-controlled border crossing at Kerem Shalom.
There have been a spate of kidnappings, armed takeovers of government buildings, and gun battles in Gaza since Israel withdrew in September after 37 years of occupation.