Gill has been battling an illness and was sidelined from India's opening match against Australia at the World Cup in Chennai.
India released a statement on Monday advising that the right-hander will remain in Chennai and not travel to Delhi for the hosts' next match of the World Cup.
"Team India batter Shubman Gill will not be travelling with the team to Delhi on 9th October 2023," the statement read.
"The opening batter who missed the team’s first fixture in the ICC Men’s Cricket World Cup 2023 against Australia in Chennai is set to miss the team’s next fixture against Afghanistan in Delhi on
the 11th of October.
"He will stay back in Chennai and will be under the supervision of the medical team."
Gill has been one of India's best performed ODI players in recent times and has risen the ODI Batter Rankings and is now in second place only behind Pakistan skipper Babar Azam.