The remains were taken from the massive mausoleum in the West Bank city of Ramallah where Arafat was buried and moved to a nearby mosque so Palestinian doctors could take samples from his bones, the officials said. Under Islam, only Muslims can handle a Muslim's remains.
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.
Arafat's body was expected to be immediately re-buried with full military honors, CBS News correspondent Allen Pizzey reports.
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.
Palestinian official Mahmoud Labadi is in no doubt Arafat was the victim of foul play and believes the late leader was poisoned, Pizzey reports.
"This exhumation reveals the facts and reveals that Arafat's death was not natural death," Labadi told CBS News.
Not everyone is in favor of the exhumation, Pizzey reports.
"My opinions are of little importance," Arafat's sister Khadija Arafat told CBS News. "Me and many other people think that there are many things more important than exhumation."
The results of the investigation aren't expected for months.
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.