The samples will be handed over to French, Swiss and Russian experts who have flown in for the exhumation and who will examine them in their home countries, the officials said. Earlier, samples were also taken from Arafat's bedroom, office and personal belongings, they said.
The Palestinian officials spoke on condition of anonymity because they were not authorized to discuss the matter with the media.
The new investigation into Arafat's death was sparked earlier this year by the discovery of a lethal radioactive substance, polonium, on clothing said to be his.
Arafat died in November 2004 in a French military hospital, a month after suddenly falling ill. While the immediate cause of death was a stroke, the underlying source of an illness he suffered in his final weeks has never been clear, leading to persistent speculation in the Arab world that Israel poisoned him. Israel has denied such allegations.
The exhumation might not resolve the mystery. Polonium-210 decomposes rapidly, and some experts say it is not clear whether any remaining samples will be sufficient for testing.