The work is expected to take up to two weeks. Mr Arafat's remains are to be exhumed by French, Swiss and Russian investigators to check for a radioactive substance, polonium-210.
The investigation came after a Swiss lab this year discovered traces of the deadly isotope on some of Mr Arafat's clothes, sparking new suspicions that he was poisoned.
The Palestinian officials spoke on condition of anonymity because the work at the gravesite is shrouded in secrecy, amid cultural sensitivities over digging up the remains of a revered leader.
Mr Arafat died in November 2004, a month after suddenly becoming ill.