"A target missile was successfully launched and tracked by the Arrow Weapon System, as part of the planned joint testing programme," the ministry said in a statement, providing no further details.
A defence ministry official was quoted by the Jerusalem Post website as saying the test was "neither a success nor a failure".
"The first part of the launch involved tracking the target missile, which was fired over the Mediterranean Sea towards Israel" in a simulated attack on Israeli airspace, Yair Ramati told the Post.
But it was decided mid-test not to fire the Arrow 3 interceptor missile, he said, citing unsuitable test conditions.
"This is not the first time that not all conditions are met for a trial," Ramati said.
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The two countries carried out similar tests in September and January, and in 2013 as Washington was considering military action against Syria.
The Arrow Ballistic Missile Defence System, designed to counter long-range missiles, has successfully intercepted missiles similar to Iran's Shihab-3 in a variety of test conditions.
Israel has been working on upgrading its missile defence capabilities to defend against long- and short-range incoming projectiles.
The Arrow project was first launched in 1988 as part of the then Star Wars programme under late US president Ronald Reagan that was abandoned in 1993.
The Jewish state accuses its arch-foe Iran of seeking to develop a nuclear weapon, a charge that Tehran denies.