Maamoun Abdulkarim confirmed there was a large explosion within its perimeter but said the basic structure of the 2,000-year-old site was intact.
But the extent of the damage is unclear with witnesses unable to get close to the temple.
Initial reports said the site had been partially destroyed.
Mr Abdulkarim, head of the Syrian Department of Antiquities and Museums, said "our information is provisional, but it indicates that any damage done was partial, and the basic structure is still standing".
Last week, IS blew up the much smaller Baalshamin temple at the site. However, Mr Abdulkarim says that the explosion at the Temple of Bel was "different" to the "huge quantity of explosives" used to destroy the Baalshamin.
However, he said they would have to wait for pictures to emerge as "witnesses can't get close enough to be sure what damage was done."
It was several days after the initial reports of the destruction of the Temple of Baalshamin that IS itself put out pictures showing its militants blowing up the site.
One Palmyra resident earlier told the Associated Press news agency there had been "total destruction" at the Temple of Bel.
The UK-based Syrian Observatory for Human Rights monitoring group said parts of the ancient temple had been destroyed.
IS militants seized control of Palmyra in May, sparking fears for the World Heritage site.
The world-famous Greco-Roman ruins are in the desert north-east of the Syrian capital, Damascus.
The Temple of Bel is dedicated to the Palmyrene gods and was one of the best preserved parts of the ancient city.
IS has previously targeted historical sites in areas under its control in Iraq and Syria, regarding their ancient temples and sculptures as heretical.
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Palmyra's ancient Temple of Bel is still standing despite an attempt by Islamic State (IS) militants to blow it up, Syria's antiquities chief has said.