About seven hours after the drama began the man released one hostage, public broadcaster NHK reported.
Television footage showed a woman walking away from the bank as night fell, escorted by a police officer and apparently handcuffed.
She was not immediately identified and the reason for the handcuffs was unclear.
The hostage-taking happened at the Zoshi branch of the Toyokawa Shinkin Bank in the central prefecture of Aichi in the early afternoon, a police spokesman said without elaborating.
Local media said the man, wielding a survival knife, took four employees and a female customer captive and was demanding the Noda cabinet step down as well as asking to speak to journalists.
Noda last week called an election for December 16. He is expected to lose, with polls suggesting the main opposition Liberal Democratic Party will be the biggest party.
The hostage-taker was originally said to be in his 30s or 40s but later reports suggested he was in his 50s.
NHK said there was no report of injuries to the hostages and the man had made no demands for money.
However, he was asking for 10 days’ worth of food and water. Broadcasters said he had also demanded cigarettes and a lighter. Shutters were down all over it but lights could be seen inside.
TV footage showed the area around the bank sealed off and guarded by police.