The remarks by Abbas Araqchi, who is also Iran's lead negotiator in talks with world powers, came a week before negotiations were to resume on a comprehensive accord over Tehran's nuclear ambitions.
"Iran's defence-related issues are not up for negotiations," Araqchi said, according to media reports.
"We will not discuss any issue other than the nuclear dossier in the negotiations," he added.
US lead negotiator in the talks, Wendy Sherman, last week told a Senate hearing that Iran's ballistic missile programme would be addressed in the comprehensive deal.
Western nations and Israel have long suspected Iran of covertly pursuing nuclear weapons alongside its civilian programme, allegations denied by Tehran.
Tehran insists its programme -- boasting long-range missiles with a maximum range of 2,000 kilometres, enough to reach Israel -- is an integral part of its defence doctrine.
It also denies ever seeking atomic weapons, saying its nuclear activities are for peaceful medical and energy purposes.
Iran struck an interim nuclear deal with world powers in November under which it agreed to roll back parts of its nuclear work in exchange for the release of billions of dollars in frozen assets and limited relief from crippling sanctions.
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