Endo was also convicted of helping to produce VX gas used to kill a second anti-cult activist, the agency said.
Waiting to die
Endo, a virology graduate of Japan's prestigious Kyoto University, became a member of the Aum Shinrikyo cult in 1987.
More than a dozen death sentences have been meted out to cult members, but none have been executed.
Shoko Asahara is currently the most
high-profile death row inmate in Japan [EPA]
Shoko Asahara, a former Aum guru, is on death row for 27 killings including 12 in the subway attack.
Prior to that, the cult amassed an arsenal of chemical, biological and conventional weapons in anticipation of an apocalyptic showdown with the government.
In 2000, Aum renamed itself Aleph.
It once had 10,000 members in Japan and another 30,000 in Russia, but authorities say membership has shrunk to about 1,650 in Japan and 300 in Russia.
The group split into factions in recent years, including one that remains close to Asahara's family.
One of his top aides, Fumihiro Joyu, set up his own 160-member sect called "Ring of Light" in May, denying he was following his master's teachings.
Japanese police say they are keeping both groups are under constant surveillance.