The process was carried out in secrecy, with Arafat's grave carefully shielded from the public eye and media kept far away, but Palestinian sources confirmed samples had been taken from the remains on Tuesday morning.
"At 5:00 am (0300 GMT), experts began to remove the stones and began opening the grave in an orderly fashion," a Palestinian source told AFP on condition of anonymity.
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The source said that only a Palestinian doctor had been allowed to directly touch the remains and remove the samples, but that the process was conducted in front of Swiss, Russian and French experts.
Palestinian officials had originally planned a military ceremony to accompany the reburial, but a source told AFP that the samples were collected from the remains without removing them from the grave, so no reburial was necessary.
"The samples were taken from Arafat's remains from inside the grave and the samples were then transferred to the mosque," the Palestinian source said, referring to a building adjacent to the Muqataa presidential complex in Ramallah, from which Arafat once ruled.
The tomb was then resealed.
For weeks now, Arafat's grave in a mausoleum on the Muqataa presidential site from which he once governed has been hidden from view by blue tarpaulins, which were torn down after the process was completed on Tuesday morning.
The samples collected are to be tested for the radioactive substance polonium as part of a new investigation into whether Arafat was poisoned.
The probe was prompted by an investigation carried out by the Al-Jazeera news channel, which commissioned a Swiss lab to test personal effects belonging to the late leader that were given to them by his widow Suha.
The tests revealed the presence of the toxic substance polonium, and prompted calls for the exhumation of Arafat's remains for new testing.
Polonium was the substance that killed Russian ex-spy and fierce Kremlin critic Alexander Litvinenko in London in 2006.
France opened a former murder inquiry into Arafat's death in late August at Suha's request, and French judges in charge of the investigation arrived in Ramallah on Sunday to participate in the exhumation process.
Rumours and speculation have surrounded Arafat's death ever since the quick deterioration of his health before he died at the Percy military hospital near Paris in November 2004 at the age of 75.
Doctors were unable at the time to say what killed the Palestinians' first democratically-elected president and an autopsy was never performed, at his widow's request.
But many Palestinians believed he was poisoned by Israel -- a theory that gained ground in July following the Al-Jazeera report.
The samples taken Tuesday will be flown to laboratories in the three countries involved, with results expected within several months.
Some experts, however, have questioned whether anything conclusive will be found because polonium has a short half-life.
Jean-Rene Jourdain, deputy head of human protection at the French Institute for Radiological Protection and Nuclear Safety (IRSN), said it would take weeks of analysis to be sure that the traces were man-made polonium rather than just coincidental contamination by naturally-occurring polonium.
"Even if traces of polonium are found, it doesn't mean that they are man-made," he told AFP.
