Coronavirus fears left the nation's normally jam-packed bullet trains and expressways deserted on the first day of Golden Week on Saturday as the pace of infections showed little sign of slowing.
Many of the shinkansen leaving Tokyo Station Saturday were over 90 percent empty, railways said.
Golden Week, a string of several closely timed national holidays, is traditionally one of the busiest times of year for the tourism industry.
"I work in the finance industry and Golden Week is almost the only time I can go back home," she said.
Under the declaration, which lasts through the last day of Golden Week on May 6, governors can take strong steps to curb the pneumonia-causing virus.