Thirteen members of the group had received death sentences. The first seven, including cult leader Shoko Asahara, were hanged about three weeks ago.
The cult, which envisioned overthrowing the government, amassed an arsenal of chemical, biological and conventional weapons in anticipation of an apocalyptic showdown. Its name Aum Shinrikyo means Supreme Truth.
The group's most notorious crime was the subway attack in 1995 that sickened 6,000 people and caused panic during the morning commute. The attack woke up a relatively safe country to the risk of urban terrorism.
Justice Minister Yoko Kamikawa called it a terrorist attack that even terrified people overseas. She said at a news conference that the six executed Thursday had collaborated with Asahara and other cult members systematically to conduct an unprecedentedly heinous crime that should never be repeated.
The cult had claimed 10,000 members in Japan and 30,000 in Russia. It has disbanded, though nearly 2,000 people follow its rituals in three splinter groups, monitored by authorities.