The rejection appeared on Rafsanjani's personal website after ultra-conservatives demanded the 79-year-old former two-time president clarify his stance on Syria.
"Recent quotes (attributed) to me regarding Syria... are absolutely not true," Rafsanjani was quoted as telling a crowd of war veteran families.
He echoed Tehran's official opposition to moves by the United States to launch military strikes against President Bashar al-Assad's government in response to its suspected chemical attacks near Damascus that are said to have killed hundreds of civilians on August 21.
"Unfortunately the people of Syria - who have been for about two years struggling with civil war as well as different kinds of pain and have been unprecedentedly displaced - are now the target of a foreign threat under the excuse of not yet confirmed use of chemical weapons," Rafsanjani said.
Tehran provides Damascus with material and intelligence support but denies accusations of arming the Assad regime to fight the uprising-turned-civil war since 2011 that has claimed more than 110 000 lives.
It has backed claims in Damascus that rebels, not the Assad regime, may have carried out the chemical attacks.
The Iranian establishment and the government of new moderate President Hassan Rowhani, in particular Foreign Minister Mohammad Javad Zarif, have voiced opposition to any military action against Syria.
The issue of chemical weapons is highly sensitive in Iran, which was the target of deadly gas attacks during its 1980-1988 war with Iraq.
Rafsanjani also "strongly condemned" US threats to attack Syria, according to his website.
"The use of weapons of mass destruction, including chemical, by any individual, group, government in all religions and schools, particularly in Islam, is rejected and condemned.
"It was Western governments which supplied Iraq with such weapons, and gave the green light for their use," he charged.
Rafsanjani was responding to a report by the unofficial ILNA news agency which had quoted him as saying: "The Syrian people who were the target of a chemical attack by the authorities must now face the threat of foreign intervention."
The agency quickly deleted from the quote the words "by the authorities", and the foreign ministry later denied Rafsanjani had made such remarks.
But some conservative websites took the opportunity to attack Rafsanjani, publishing online a video of a public meeting at which Rafsanjani is alleged to have made the comment.
Even though it was not possible to identify that the speaker on the video, shot from some distance using what appeared to be a low-tech cellphone, the voice sounded like Rafsanjani's.
"We are waiting for a denial from Rafsanjani in person and the taking of a clear position," conservative lawmaker Alireza Zakani was quoted on Thursday as saying and demanding an investigation by the intelligence ministry.
On his website on Saturday, Rafsanjani criticised those reactions, and berated without elaborating "some domestic media for falling in line with enemy objectives only to preserve the political interest of their parties".