"I am painfully aware of my responsibility," Aoki told a committee in Parliament.
Foreign Minister Yukihiko Ikeda, speaking before the same committee, said he would accept the resignation. No replacement was immediately named.
Ikeda said he would let Aoki step down before the results of a government investigation into the incident are released. The investigation is expected to conclude next month.
Aoki was called before the committee to answer a series of criticisms for the crisis, which began Dec. 17 when leftist rebels stormed a gala reception Aoki was holding to celebrate the birthday of Japan's Emperor Akihito.
Aoki and 71 other hostages were freed by Peruvian commandos four months later. He was injured in the raid and still uses crutches to walk.
Though all the rebels, two soldiers and one hostage died in the raid, none of the 24 Japanese hostages was killed or seriously injured. Aoki's role in keeping the situation from leading to more blood-shed was initially hailed by Japan's government and media.
That praise, however, was quickly replaced by angry attacks in Parliament and in the press.
Critics slammed Aoki for everything from not ordering enough security before the attack to chain-smoking through a news con-ference held shortly after his release.
Over the past week, popular weekly magazines have quoted unidentified former hostages as saying Aoki was a coward who treated them with a mixture of rudeness and arrogance.