In a statement, Israeli police said they arrested six people for allegedly violating public order and attacking officers.
Police accused “hundreds of rioters” of disrupting public order before and during the funeral by chanting nationalist slogans and throwing stones at them.
Police had to “disperse and repel” the crowds as well as make arrests, the statement said, “in order to allow the funeral to take place legally.”
But the police were condemned by Dr. Mustafa Barghouti, the secretary-general of the National Initiative Movement political party, who called their actions a “brutal assault.”
Police later allowed the family to drive the casket to a Catholic church in the Old City, which was packed with mourners, before sealing off the hospital and firing tear gas at scores of protesters inside, according to The Associated Press.
Crowds chanted “We die for Palestine to live” and sang the Palestinian national anthem, a rare mass show of Palestinian nationalism in east Jerusalem — the contested part of the holy city that Israel captured in 1967 and which the Palestinians claim as their capital.
Israel says east Jerusalem is part of its capital and has annexed the area in a move that is not internationally recognized.
Abu Akleh, 51, was fatally shot Wednesday morning while covering raids in the West Bank for Al Jazeera, with the broadcaster and another reporter who was wounded in the incident blaming Israeli forces.
The veteran Palestinian American journalist had spent a quarter century covering life under Israeli military rule, which is now into its sixth decade.
