Shanto made the decision after consulting the Bangladesh Cricket Board’s (BCB) medical department as he had returned to Bangladesh’s T20I setup through the Asian Games.
National team physiotherapist Bayjedul Islam Khan said: “Shanto had been suffering from fever since we landed. It has been four days already, but the fever has persisted. It is a low-grade fever, and tests conducted here have confirmed evidence of an infection, although he has tested negative for influenza and COVID-19.
“He is understandably very weak and is not expected to recover in time to play any part in these Games. Therefore, he is flying back home.”
The left-hander had previously been dropped from the T20I side primarily due to concerns over his strike rate.
Meanwhile, southpaw Shamim Hossain set to replace unwell Shanto in the squad.
Ten teams are taking part in the men's cricket event at the 20th Asian Games. Bangladesh, India, Pakistan and Sri Lanka received direct entry into the knockout stage, while Afghanistan, Hong Kong, Japan, Malaysia, Nepal and Oman competed in the first round.
The men's cricket event began on September 24, with the final scheduled for October 3.