Putin in comments to his national Security Council expressed "deep concern over such a decision and once more stressed the importance of this document," the Kremlin said, referring to the deal.
Putin later held talks with Netanyahu, who has backed Trump's decision on Iran, Israel's arch-foe.
Netanyahu before leaving Israel for the visit said that "the meetings between us are always important and this one is especially so".
The leaders' initial remarks, published in a transcript by the Kremlin, did not refer to the Iran nuclear deal directly.
Putin said the meeting would discuss "problems in the region," saying that "the situation unfortunately is very acute".
"I want to express a hope that we will manage not just to discuss but also to seek a solution that would lead to a shift in the situation," Putin said.
Netanyahu said they would "think together how we can act correctly in the region, how we can remove the threats that exist in the region in a responsible and reasonable way".
The two leaders earlier Wednesday watched a Red Square parade marking the anniversary of victory over Nazi Germany in World War II.
Netanyahu thanked Putin for referring to the Holocaust in his parade speech, likening the Nazi extermination campaign to Iran's attitude to Israel.
"But there is a difference between what was then and what is today: we have our own country," he added.
Russia's foreign ministry said late Tuesday it was "deeply disappointed" by Trump's announcement that the United States would pull out of the Iran deal, while Netanyahu strongly supported the US president's "bold" move.
Moscow and Tehran have close political and economic relations.
In the nuclear field, Russia has already built one reactor at Iran's Bushehr plant, the country's only nuclear power plant, and has started work on two new ones.
By contrast Netanyahu on Monday held a televised presentation of what he called "proof" of Iran's alleged past military nuclear ambitions.
Netanyahu and Putin have held a series of meetings and phone conversations in recent months, particularly related to the conflict in Syria where Israel has vowed to prevent Iran building a military presence.
(This story has not been edited by NDTV staff and is auto-generated from a syndicated feed.)