The late-June qualifying event was to be held in Taiwan, but was moved to Mexico after the Taiwanese government limited foreign arrivals in the face of an outbreak.
“We worked through multiple options and scenarios but the logistical challenges of providing a safe environment for the group were insurmountable,” Williams said.
“Even if Team Australia were successful in winning the event, the timing didn’t allow for the team to complete quarantine in Australia and meet the requirements of entry to the Tokyo games.
The Chinese and Chinese Tapei teams have also pulled out of the Olympic qualifiers, according to Baseball Australia.
Baseball is returning to the Olympics for the first time since Beijing 2008. Australia won a baseball silver medal at the Athens Olympics in 2004.
Hosts Japan, Israel, Mexico, South Korea and the United States have already qualified for the Tokyo Games baseball event, with the Dominican Republic, Venezuela and the Netherlands competing for the final berth at the Mexico qualifying tournament, which will be held June 22-26 in Puebla.