Macron told Netanyahu it was important to keep the deal and called for "the necessary respect by all parties of their engagements regarding the accord", a presidential statement said after the call on Saturday.
The statement was a rebuff for Netanyahu, who had said "Trump's remarks should be taken seriously and whoever wants to keep the nuclear deal would be wise to fix it," according to a statement from his office.
The free world should "strongly condemn the five crimes of the Iranian regime", Netanyahu added, listing "efforts to obtain nuclear weapons... developing ballistic missiles... supporting terror... regional aggression" and "the cruel repression of Iranian citizens".
Macron, who called on Trump not to pull the US out of the deal this week, did add that it was "necessary to work on the ballistic aspect and Iran's regional activities", saying that France has proposed doing so since September last year.
Israel accuses Iran of wanting its destruction, supporting global terror and meddling in Lebanon and the Palestinian territories.
Iran's foreign affairs ministry on Sunday said in a statement that the Islamic republic would renegotiate the agreement.
Netanyahu arrives in India
Netanyahu arrived in India on Sunday, to be met at the airport by Prime Minister Narendra Modi, whom he hailed as "a close friend of Israel and of mine".
He is accompanied by 130 entrepreneurs, the lagest-ever business delegation to travel with and Israeli leader.
India is Israel's biggest arms market, buying around a billion euros' worth of weapons every year.
But Delhi receently cancelled a half-billion-dollar order to buy Israeli Spike anti-tank guided missiles because a state-run defence contractor offered to make similiar missiles locally.
Deals for gas and oil cooperation, cybersecurity and agricultural projects are on the agenda.
The six-day visit is the first by an Israeli leader for 15 years.