Fumio Kishida, who was accompanied by Japanese business executives, said a cooperation council was to be set up with Iran's government to improve contacts between ministries.
"We want to benefit from this opportunity," he said at a joint press conference with Iran's Foreign Minister Mohammad Javad Zarif.
"We are looking at what we can do to capitalise on the nuclear deal."
A new cooperation agreement would speed up new ventures, Kishida said.
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Today's visit was the first time a Japanese foreign minister had been accompanied to Iran by business delegates since the Islamic revolution in 1979, according to Kishida.
In later meetings today, he and Zarif would discuss the situation in civil war-torn Syria and other violence in the Middle East, he added.
The nuclear deal between Iran and six world powers (Britain, China, France, Russia and the United States plus Germany) was agreed on July 14. Its implementation is due by the end of 2015.