The 20-year-old has started in all of Liverpool's last six matches but suffered a hamstring injury during the club's 3-1 victory over Cardiff City last Saturday.
The 20-year-old left back has started in all of Liverpool’s last six matches after Jose Enrique required surgery on a knee injury which has sidelined the Spaniard until February.
Flanagan was substituted after 55 minutes in Liverpool’s 3-1 win over Cardiff City on Saturday and Rodgers has revealed the defender will undergo a late fitness test ahead of the fixture at the Etihad Stadium.
"Our squad is very thin at the moment, 17 players - which is unfortunate for us coming into a busy period. We just have to assess young Jon Flanagan,” Rodgers told reporters. "Leading into the game against Cardiff he had a tight hamstring for a few days. He was fit enough to start and play. He felt it a little bit in the game so obviously we had to take him off.
"We just need to assess how that is over the next 24 hours. At the moment, none of the guys who have been out have returned, so we're quite thin on the ground."
Although Rodgers is having to deal with an extensive injury list over the busy festive period he is keen to continue the team's momentum and is likely to give some youngsters a chance to impress.
"These games are opportunities for us. We're not going to cry about it," added the Liverpool boss. "We have what we have, the players have been absolutely brilliant and we know we have got a busy schedule now.
"It's an opportunity for me to bring in some youth-team players and reserve-team players into the squad. That's why you have an academy."