According to ministry spokesman, Hossein Jaberi Ansari, the missiles were "conventional defensive instruments and they were merely for legitimate defense," the official IRNA news agency reported.
Iran's Revolutionary Guard test-launched two ballistic missiles on Wednesday emblazoned with the phrase "Israel must be wiped out" in Hebrew — a show of power by the Shiite nation, long an opponent of Israel.
It was the latest in a series of recent tests, aimed at demonstrating Iran's intentions to push ahead with its ballistic program after scaling backing its nuclear program under the deal reached last year with the U.S. and other world powers.
Ansari said the test-firing "did not defy the Security Council resolution" and added that Iran will continue its missile program. However, he also said Iran will remain committed to its international obligations.
"The Islamic Republic of Iran will not compromise over its security and defensive power," said Ansari.
"It will continue it's completely defensive and legitimate missile program while observing its international commitments and without entering into the fields of either nuclear warheads or designing missiles capable of carrying such warheads," he added.
The landmark nuclear deal, under which Iran accepted to substantially cap its nuclear program, does not include provisions against missile launches.
When it came into effect on Jan. 16, the Security Council lifted most U.N. sanctions against Tehran — including a ban it had imposed in 2010 on Iran testing missiles capable of carrying nuclear warheads.
That ban likely would have covered some of the missile fired this week.
To deal with the restrictions in the nuclear agreement, the U.N. Security Council adopted a resolution last July which among other measures "calls on" Iran not to carry out such tests.
Late Wednesday, the head of the airspace division of Iran's powerful Revolutionary Guard, Gen. Amir Ali Hejazi, told state TV that the Hebrew markings on the missiles tested earlier in the day were "a choice by colleagues" who worked on the missiles, indicating it was not an official, high-level decision.