Makoto Hirata, 46, was wanted for the abduction and murder of a notary official on March 1, 1995, the Kyodo news agency said.
Hirato was a senior member of the Aum Shinrikyo. or AUM, doomsday cult responsible for the deadly 1995 sarin nerve gas attack on the Tokyo subway, CNN said. At least 13 people died in the gas attack and more than 1,000 others were injured.
There was no indication as to what prompted Hirata to surrender.
The charges against him include abduction, conspiracy to confine the notary and injecting him with a lethal chemical, Kyodo said.
During the 1990s, the AUM group issued statements saying the world was soon to end and advocated extreme measures to prepare for it.
Several of its senior leaders are in jail, although the organization still exists and describes itself as a benign religious group, CNN said.