Tokyo said it would provide 102.8bn yen ($862m; £437m) in loans to repair Iraqi oil pipelines, export facilities and power supply infrastructure.
A further 57.7bn yen for water and electricity projects was also agreed on Iraqi Prime Minister Nouri Maliki's four-day trip to Japan.
Japan depends on the Middle East for nearly all of its crude oil.
Mr Maliki also met with Emperor Akihoto and thanked Defence Minister Fumio Kyuma for Japan's efforts in support of Iraq.
He urged Japanese companies to return and make investments in the war-torn country. Following positive talks with business leaders, he was upbeat about the prospect of co-operation.
His visit to Tokyo comes two weeks after Iraqi Vice President Tareq al-Hashimi was in Japan and said US-led coalition forces should not be withdrawn until Iraq's army is fully trained and ready to take over security.
Tokyo backed the US-led invasion of Iraq in 2003 and provided troops for a non-combat, humanitarian mission in the southern city of Samawah.
It withdrew its ground forces last July, but last month Japan's Cabinet approved a two-year extension of the country's air mission in Iraq after its expiry date lapses in a few months.