Aguero was replaced at half-time in Manchester City’s 5-0 win over Burnley in the league on Monday night, helping them close the gap on leaders Liverpool to 19 points.
The Argentina international was injured under a tackle from Burnley’s Ben Mee late in the first half which won City the penalty for their third goal on the night, with Aguero not returning after the break.
“It doesn’t look good,” City boss Pep Guardiola said.
“It is something in the knee. We will see tomorrow and will see what he has.
“He felt something in his knee and he will struggle in the last month, but we will see.
“The doctor said tomorrow we will know more, but it doesn’t look good at this moment.”
Riyad Mahrez and Phil Foden both scored doubles in the win, while David Silva scored the other goal as City completed a perfect double win restart to the league after their midweek 3-0 win over Arsenal.
Guardiola was especially pleased with Foden, who has had limited opportunities all season, but scored three times in two matches.
“I’m happy with him and if he feels its his best performance - perfect,” Guardiola said.
“I said many times, he’s never played bad. Especially for his behaviour and attitude. On the pitch, training, he loves to play football.
“He plays every time with us since he was promoted to be the senior squad and has played a high level. We cannot forget he is just 20 years old. He will be decisive player for this club.”
City are next in action against Chelsea on Thursday in the league.