Khamenei said there was no base for international concerns. He said the development and use of nuclear weaponry violates beliefs held by Iranians, the BBC reported.
"The West's accusations are baseless because our religious beliefs bar us from using such weapons," Khamenei said.
"We do not believe in atomic weapons and are not seeking that," he said.
Khamenei's comments followed a recent report by the International Atomic Energy Agency that Iran is cooperating less with he atomic watchdog agency.
The report prompted the United States to warn of consequences for Iran if the country fails to accept its international responsibilities, the BBC reported.
Officials in Germany and Britain said the report made them concerned that Iran may be taking part in nuclear activities such as uranium enrichment.