Russian President Vladimir Putin (L) and UN chief Antonio Guterres
The conversation "mainly focused on implementing the Istanbul agreements on exporting Ukrainian grain" from Black Sea ports, and the export of Russian food and fertiliser, the Kremlin said.
"Both sides emphasised the importance of meeting the needs, as a priority, of those in Africa, the Middle East and Latin America who need food," the Russian presidency said in a statement.
The Kremlin has repeatedly criticised the landmark deal allowing grain exports from Ukraine, brokered by Turkey and the United Nations in July.
Moscow says its own exports have suffered, and Putin last week claimed most of the consignments were arriving in Europe, not poor countries where grain was needed most.
Ukrainian officials have denied the claim and data compiled by a monitoring group as part of the accord does not reflect Putin's assertion.
The Kremlin said Guterres "provided detailed information on the efforts made... to remove all obstacles" to Russian exports, saying he was "fully committed to resolving this problem".
Putin is set to meet Turkey's president in Uzbekistan on Friday, where the Kremlin has said they will discuss the deal.
During the call with Guterres, Putin also hailed "constructive cooperation" with the UN's nuclear watchdog over Ukraine's Zaporizhzhia plant.
Shelling around the Russian-controlled facility in southern Ukraine has raised fears of a nuclear disaster.
The International Atomic Energy Agency (IAEA) inspected the plant in early September following repeated bombardment.
The Kremlin said that "Putin made a positive assessment of the constructive cooperation with the agency".