Central committee member Amal Hamad waited at the Palestinian side of the Erez crossing for two hours before she was turned back, Fatah said on Monday.
She was meant to travel to a central committee meeting in the West Bank, the party said, accusing the Hamas government of deliberately trying to weaken the Fatah movement in Gaza.
Hamas' interior ministry said that Hamad did not wait long enough at the Erez crossing and left before her travel procedures had been completed.
She is free to leave Gaza via Erez whenever she likes, the ministry added.
In March, Hamad said she canceled a trip to Ramallah when Hamas police at the crossing insisted she be subject to a physical inspection.