In a statement on Sunday, Bahram Qassemi offered Iran’s sympathy to the Japanese government and nation over the “bitter” natural disaster that has killed dozens of people and left many others missing in recent days.
At least 66 people have died and many more are missing in floods and landslides across much of western Japan.
Hiroshima Prefecture was hit the hardest with numerous landslides that killed at least 15 people and authorities have warned that the death toll will continue to rise.
Almost 5 million people have been told to evacuate as homes have been destroyed and cars swept away.
Since the downpour began on Thursday, the weather agency of Japan has forecasted record amounts of rain through Sunday, warning of flooding, mudslides and lightning strikes.
Japan's Meteorological Agency retained special weather warnings for three prefectures on the main island of Honshu, down from five, and urged vigilance against landslides, rising rivers and strong winds amid what it called "historic" rains.