Gill, who was set to join the India A squad in Visakhapatnam on Wednesday, injured himself at a training session in Mohali prior to joining Punjab's pre-season camp, ahead of their Ranji Trophy opener on October 6.
"I've been advised bed rest for a week after which there will be a fitness assessment," Gill, for whom this was also a maiden call-up to Punjab's Ranji side, told ESPNcricinfo. "I'm trying to get fit soon."
Gill impressed for India Under-19s across formats during their tour of England in July. He was the top-scorer of the one-day series, making 278 runs in four innings at a strike rate of over 100. He also struck a match-winning century in the second youth Test that preceded the one-dayers.
The England tour was preceded by a breakout home series against the same opposition earlier in the year, when Gill dominated the one-dayers with 351 runs at an average of 117, despite playing only four of the five games. That included back-to-back centuries in the third and fourth games in Mumbai.
Meanwhile, the BCCI has amended the Board President's XI squad to include the legspinner Rahul Chahar in place of his seam-bowling brother Deepak Chahar. The original squad announced on Monday had erroneously contained Deepak's name instead of Rahul's.
India A team for first three one-day games: Prithvi Shaw, Mayank Agarwal, Shreyas Iyer (capt), Deepak Hooda, Shreevats Goswami (wk), Shahbaz Nadeem, Karn Sharma, Vijay Shankar, Shardul Thakur, Siddarth Kaul, Mohammed Siraj, Basil Thampi, Ankit Bawne
India A team for last two one-day games AR Easwaran, Prashant Chopra, Deepak Hooda, Shubman Gill, Baba Aparajith, Rishabh Pant (capt & wk), Shahbaz Nadeem, Karn Sharma, Vijay Shankar, Shardul Thakur, Siddarth Kaul, Mohammed Siraj, Basil Thampi.
Board President's XI Prithvi Shaw, Shivam Chaudhary, Shreyas Iyer (capt), Karun Nair, Gurkeerat Mann, Milind Kumar, Rishabh Pant (wk), Shahbaz Nadeem, Rahul Chahar, Dhawal Kulkarni, Jaydev Unadkat, Avesh Khan.
0410 GMT The story was updated to include the change in the Board President's XI squad