Russian President Vladimir Putin and Israeli President Isaac Herzog discussed the strained relations between their countries and the situation of the Jewish Agency in Russia in a phone call on August 9.
The Russian Justice Ministry has moved to disband the agency's Russian arm, which promotes emigration to Israel, despite protests from Israel.
Russia accuses the organization of violating the country's laws and, according to media reports, unlawfully collecting personal data from Russian citizens.
Some Israelis have seen this as retribution for Israel's criticism of Russia's military campaign in Ukraine.
The case against the Jewish Agency is due to be heard on August 19.
The discussion was "open and honest," Herzog's office said, adding that Herzog spoke at length about the activities of the agency.
Herzog was chairman of the Jewish Agency before he took over as president.
"The two presidents emphasized the important areas of cooperation between Israel and Russia, and agreed to stay in touch," Herzog's office announced.
Putin, he said, had stressed his personal commitment to remembrance of the Holocaust and the fight against anti-Semitism.
Kremlin spokesman Dmitry Peskov confirmed that the phone call also touched upon the Jewish Agency. Both sides had agreed that "contacts on this will continue along the responsible authorities of both countries," he said.
Peskov rejected reports that the dissolution of the organization was intended to prevent the departure of bright minds from Russia.