"As we have said on several occasions and contrary to certain statements, Iran has no programme to build a Shahab-4 missile," the statement was quoted as saying.
It was not clear what provoked the defence ministry to issue such a statement.
During a major military parade on September 22, Iran showed off six of its Shahab-3 missiles which were decorated with anti-Israeli and anti-US slogans.
According to a commentary given over loud-speakers lining the parade route, the missiles have "a range of 1,700 kilometers" (1,060 miles) and "are capable of hitting the heart of the enemy".
The development of these missiles has sparked widespread alarm in Israel.