The assembly's call targets the Japan-US Status of Forces Agreement, urging the US military to prevent such incidents. A separate statement to the same effect was addressed to the Japanese government.
Ryotaro Odo, who heads the assembly's special committee on US military bases, said the US military was "not functioning as an organisation", pointing to failures in training and discipline. He described the killing as "extremely heinous and despicable" and urged the military to cooperate with investigators and discipline those responsible.
Some assembly members opposed the resolution because it failed to demand the dismissal of the US military chief in Okinawa, according to Japan's Kyodo News agency.
Lance-Corporal Devin Jacob Ballard, 20, has been accused of killing Anna Yagi, 39, at a hotel in Naha on Saturday. He has denied the allegations. The case has sparked demonstrations in Tokyo and Okinawa.
Okinawa hosts the majority of the 54,000 US soldiers stationed in Japan. Crimes including rapes, assaults, hit-and-run and drink-driving incidents by US personnel have long sparked protests.
The US military paused operations for 48 hours from Wednesday and imposed a 30-day curfew from midnight to 5am starting on Friday. Tokyo has called in the US ambassador and the US forces commander in Okinawa to protest the incident, and Prime Minister Sanae Takaichi has condemned the "heinous" crime.
Okinawa, under US control from 1945 to 1972, still hosts many facilities used exclusively by US forces. The island's assembly passed a similar resolution in 2024 after a series of sexual assaults by US servicemen came to light, with municipal assemblies in Naha, Ginowan, Miyakojima and Motobu filing protests.