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The country's 12 professional baseball teams, divided into two leagues, were scheduled to play six games across Japan, the first major professional sport in Japan to return to action since the pandemic.
J-league top-flight football will resume on July 4 after the season was suspended in February.
Japanese baseball's top official Atsushi Saito said safety would remain his primary concern, but vowed to bring back fans in the future.
"We apologise that the season has to be opened behind closed doors, but we promise that we will continue to work toward creating an environment where, if conditions permit, we will invite fans to ball parks to enjoy watching," he said in a statement.
"We would be honoured if the start of the professional baseball season can serve as a guide for reopening other sports and entertainment," Saito added, with baseball and football both seen as a marker for other events such as concerts.
Saito said he hoped the resumption of baseball would "lift the spirits" of some of the world's most enthusiastic fans.
The government has lifted a national state of emergency imposed to contain the virus, but the public are still urged to observe good hygiene practices and social distancing.
Baseball in Taiwan and South Korea has been played behind closed doors for weeks.
The pandemic has already forced a one-year delay to the summer Tokyo Olympics, and suspended everything from sumo to the summer high-school baseball tournament - an enormously popular event that receives extensive television coverage.
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