The Argentina striker suffered a knee injury in training during March and missed the games against Stoke, Everton and Liverpool.
He returned for last weekend’s derby against Manchester United but after suffering a heavy challenge from Ashley Young could only manage the final 25 minutes of Tuesday’s Champions League quarter-final.
Pep Guardiola says he will not be considered for the game against Spurs - and with John Stones and Benjamin Mendy still sidelined through injury and Fernandinho missing through suspension, it leaves the City boss with limited options.
“Aguero is injured,” Guardiola confirmed. “He was injured before the game [against Liverpool] but tried to help us. That's why he could not play from the beginning. He was not ready.
“I don’t know [when he will be back]. You cannot forget he was injured and he made a huge effort because after the action from Ashley Young against United, the problem in the knee he could not train.
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“He played less than 15, 20 minutes and after said he cannot run and was in a lot of pain. I don’t if he will be ready for Swansea.
"Hopefully for the last games we can have him.
“John Stones is not ready. Fernandinho is suspended. Mendy is out. We have 14 players for the next game, plus the kids.”
City are currently on a three-game losing run for the first time under Guardiola.
It’s been a difficult week for the Club, with a crushing Manchester derby defeat and a Champions League quarter-final loss to Liverpool.
But Guardiola says his players need to remain calm and approach each game in exactly the same way they have throughout the rest of the campaign.
“Try to be who we were during the season and thinking about three points,” he said. “We are 13 points clear because we deserve to be there.
“In the last eight or nine Premier League games, we lost one. We won the last five in a row before United. Results are good.
“We need to think about the strong points of Tottenham, try to win the game.
“One of the successes we have had is when we drop points, we have then win, win, win, win."