Zarif met Kono in Yokohama, south of Tokyo, on the first of his two-day Japan visit and said the two countries were keen in keeping the energy market stable, which in turn made it important to maintain security in the Persian Gulf.
The meeting had not been announced by the Japanese government until Tuesday itself and follows intense diplomatic activity by Tehran in the last two days, Efe news reported.
During the meeting, Kono emphasized Japan's concern over rising tensions in the Middle East and expressed Tokyo's willingness to contribute in easing tensions through diplomatic efforts.
The Japanese Minister also urged Tehran to respect the restrictions on its atomic programme established through the multilateral nuclear agreement signed in 2015, which has been jeopardized after the US withdrew from the deal in 2018 and Iran announced it would gradually stop compliance.
Kono said Iran should return to the framework of the deal as soon as possible and added that there should be a limit to the quantity and level of nuclear enrichment Tehran is allowed to carry out even if it is for peaceful means.
According to the Japanese government, Zarif will also meet Prime Minister Shinzo Abe in Yokohama on Wednesday.
In the past, Abe has unsuccessfully tried to mediate in the crisis between Washington and Tehran. But he has not yet responded to Washington's request to become a part of its coalition to protect oil tankers that pass through the Strait of Hormuz in the face of possible aggression from Iran.
( With inputs from IANS )