Israeli President Isaac Herzog spoke with Russian President Vladimir Putin on Tuesday about Russia's attempt to ban the world's biggest Jewish non-profit group, which helps Jews move to Israel.
Russia's justice ministry is seeking to liquidate the Russian branch of the Jewish Agency for alleged breaches of privacy laws.
Some Israeli politicians have expressed concern that Russia may be retaliating for Israel's criticism of its invasion of Ukraine, and about the effect that bilateral tensions might have on Russia's own Jewish community.
Some also worry that it could damage Russian-Israeli communications on Syria, where Moscow deploys air power in support of the government and Israel has attacked what it describes as Iranian-linked military targets.
"The phone call was frank and honest. The two presidents emphasized the important areas of cooperation between Israel and Russia and agreed to remain in contact," Herzog's statement said.
The Kremlin said the men had agreed that contacts about the Jewish Agency would be continued by both countries.
Some 600,000 Russians are eligible to emigrate to Israel because of Jewish heritage, and officials say there has been a rise in applications since the dispute arose.
Herzog, whose post is largely symbolic, said the call with Putin had been coordinated with Israeli Prime Minister Yair Lapid, who has condemned Russia's invasion of Ukraine.