Mourners fired guns into the air as the coffin arrived on a helicopter following a military funeral in Egypt.
Thousands surged around the helicopter, initially preventing the unloading of the coffin, before it was finally taken off, 25 minutes delayed, and borne through the crowds.
Mr Arafat, 75, died in a French military hospital early on Thursday.
A police jeep edged through the crowds to clear a space by the helicopter, as Palestinian officials accompanying the body from Egypt pleaded with the crowd to move back and allow them to open the door.
