The foreign minister will stay in Iran until Wednesday before making a quick stop in Dubai, the foreign ministry official said.
"She will offer her regret and condolences for the damage caused by the earthquake and explain what Japan is doing to help," said the official.
Kawaguchi may make a stop in other nations before returning to Japan on Friday, he said.
In Iran, the minister will discuss Japan's delivery last month of tents, blankets and plastic sheets aboard two C-130 cargo planes, and separately Japan's pledge of some one million dollars in aid, he said.
At least 30,000 people are believed to have died in a quake that measured up to 6.7 on the Richter scale, shattering the southeastern ancient city of Bam.
She will also explain Japan's decision to send troops to Iraq to help with reconstruction and humanitarian assistance.
The minister will also urge Iran to continue to cooperate fully with the International Atomic Energy Agency (IAEA) after Tehran last month signed the additional protocols of the nuclear Non-Proliferation Treaty, which opens the way for snap inspections of sites, the official said.