University of Tokyo professor Toshiso Kosako said he couldn't stay on and allow the government to set what he calls, "improper radiation limits" for elementary schools near the tsunami-damaged Fukushima Dai-ichi nuclear plant.
He also criticized the government for not disclosing radiation levels around the plant.
"I cannot allow this as a scholar," he said. "I feel the government response has been merely to bide time."
A Kyodo News service poll released Saturday showed that Prime Minister Naoto Kan's support ratings were plunging.
The poll reported that 76 percent of the respondents think Kan is not exercising sufficient leadership in handling the country's earthquake, tsunami and nuclear triple crisis, up from 63.7 percent in the previous survey in late March.
Kan appointed Kosako after the magnitude-9.0 earthquake and tsunami struck northeastern Japan on March 11. The disaster left 26,000 people dead or missing and damaged several reactors at the Fukushima Dai-ichi nuclear power plant, setting off the world's worst nuclear crisis since Chernobyl in 1986.
Meantime, the lower house of the country's parliament approved a $50 billion budget to help finance post-tsunami rebuilding efforts.
The Associated Press contributed to this report.