Hajj, the annual pilgrimage obligatory once in a lifetime for all Muslims with the means to afford it, is set to begin next week.
Religion and politics
The fate of Gaza's pilgrims has been in question for weeks amid continued political jockeying between Hamas and rival Palestinian faction Fatah.
At issue was also Saudi Arabia's recognition of the Hamas government structure in Gaza as legitimate.
Around 3,000 Gazans applied for Hajj visas through the ministry of religious affairs based in Ramallah, West Bank, while another 3,000 applied through the Gaza-based ministry.
Saudi Arabia is said to have it granted visas only to Palestinians who registered for Hajj through the Ramallah offices of the Palestinian Authority, which is run by Fatah.
Ismail Haniya, a Hamas leader who was deposed as the Palestinian Authority's prime minister last year, has urged Riyadh to issue visas to the remaining Gaza pilgrims.
He said pilgrims would be able to travel only once that had been done.
"For many Palestinians the idea that there is a siege [of Gaza] but also now Palestinians are denying each other the right to leave is extremely disheartening," Al Jazeera's Ayman Mohyeldin in Gaza City said.
"And that was reflected on the faces of the people we spoke to today."
Palestinian Authority officials accused Hamas of committing a "crime" for not allowing pilgrims with visas to leave.
"Saudi Arabia only recognises the Palestinian Authority, which represents all Palestinians in Gaza and the West Bank," Jamal Bawatma, minister of religious affairs for the Palestinian Authority, was quoted by Reuters news agency as saying.