The shells, filled with a highly toxic mustard agent, were found recently by revolutionary fighters at two sites in central Libya, The Washington Post reported Sunday.
The sites were under heavy guard and 24-hour surveillance by drones, U.S. and Libyan officials said.
The discovery prompted a U.S. intelligence-led investigation into how the Libyans obtained the shells and several sources told the Post initial suspicion indicated they came from Iran.
"We are pretty sure we know" the shells were custom-designed and produced in Iran for Libya, said one senior U.S. official, who spoke anonymously because of the sensitivity of the accusation.
Gadhafi was killed in October.
Mohammed Javad Larijani, an adviser to Iran's supreme leader, denied the allegation.
"I believe such comments are being fabricated by the U.S. to complete their project of Iranophobia in the region and all through the world. Surely this is another baseless story for demonizing [the] Islamic Republic of Iran," he said in an e-mail to the Post.
A U.S. official with access to classified information confirmed "serious concerns" were raised that Iran provided the shells to Libya years ago.
The stockpiles' existence violates Gadafi's promises in 2004 to the United States, Britain and the United Nations to disclose all of Libya's chemical weapons and begin destroying them.
Gadafi's government was "sitting on stuff that was not secure, and the world did not know about it," another U.S. official said. "There were no seals and no inventories" [by international inspectors].
The shells' disposal poses a challenge to Libya's new government and Western allies because they can't be relocated easily and could take up to a year to destroy in place, the Post said.
A senior U.S. official said the White House first heard about the shells in September. Other officials told the Post they were stored in Houn and Sabha.
One U.S. official said Iran could have sold the shells to Libya after the end of Iran's war with Iraq, in which the Iraqis used mustard and nerve agents against Iranian troops.
"These were acquired over many years" by the Libyans, another U.S. official said.