In a document addressed to Kishi, the residents also asked that Japan urge Myanmar's armed forces to restore the democratically elected government.
Also read: Japan urges Myanmar forces to stop violence against protesters
They handed the document to a Defense Ministry official after about 120 Myanmar residents and others held an anti-coup protest in front of the ministry in Tokyo.
They took the action as Myanmar security forces have killed, according to the United Nations, more than 50 people in an attempt to prevent daily demonstrations and strikes in the Southeast Asian country since the military takeover.
Also read: New charge filed on Suu Kyi as Myanmar crackdown intensifies
"We, mainly young people, gathered here to raise our voices," said Lae Lae Lwin, 30, a Myanmar nurse working in Japan.
"We know Japan has connections with the Myanmar military," she said. "We would like the Japanese government to push the military to stop its violence and change course."
Also read: Moon calls for release of Myanmar's Aung San Suu Kyi, condemns crackdown on protests
In Kobe, western Japan, some 400 Myanmar residents and others held a similar demonstration, saying they will never recognize a military dictatorship in their home country and calling for the release of Suu Kyi and other members of her National League for Democracy party.