"I love you, but please do not attack Iran. It is not the solution, it would only aggravate the situation," the well-known director said at a news conference to promote his latest film, The Gardener, at the annual Jerusalem film festival.
Forced into exile following death threats, Makhmalbaf backs a "cultural" dialogue between arch-rivals Iran and Israel which both ban citizens from travelling to each other's country.
He said it is pointless to threaten to attack Iranian nuclear facilities, which Israeli officials do regularly.
Israel and much of the West suspects Tehran wants to make atomic weapons, a charge it strongly denies.
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"It's better to help the Iranian democratic forces," Makhmalbaf said, insisting that an aggressive approach would fail.
"After more than 60 years, you (Israelis) still have not found a solution with the Palestinians because politicians on both sides are immature, they did not comprehend that the root of the conflict lies in the culture and religion."
The Bahai religion was founded in Iran in the 19th century and is anathema to the Islamic clerical regime.
The film revolves around a native gardener and other members of the Bahai community and also focuses on a dialogue between a father and his son.
"I am not religious, but it's impossible to dismiss the religious factor... And just look at the problems with a secular vision," he said.
"I chose Bahai as it has a tolerant and non-violent approach that can be an example to other established religions.