"Iran's missile power is not negotiable in any level under any pretext," Rouhani told Yukiya Amano, the director-general of the International Atomic Energy Agency, the official IRNA news service reported.
The president added, however, that Iran is prepared to cooperate with the IAEA's probe into whether its civilian nuclear program has a military component, "since there is no room for using a weapon of mass destruction in Iran's defence doctrine."
Iran's long-range missile program has long been a major concern for Israel, which fears it may one day mount nuclear warheads on the projectiles and has not ruled out military action to prevent that from happening. Iran insists the missile program is a vital deterrent to a possible Israeli attack.
Amano's visit comes as world powers continue to negotiate with the Islamic Republic in hopes of reaching a permanent deal to curb its nuclear ambitions in exchange for the lifting of crippling international sanctions.
The IAEA is trying to investigate allegations that Iran secretly worked on nuclear weapons -- something Tehran denies.
The US and its allies insist that any overall nuclear agreement with the Islamic Republic must include a conclusion by the agency that Iran has fully cooperated with its probe.