Aguero lost his place in Pep Guardiola’s starting line-up following the arrival of Brazilian starlet Gabriel Jesus in January.
The 28-year-old, who has scored 122 league goals in 181 appearances since joining from Atletico Madrid in 2011, returned to the team following an injury to Jesus and finished the season as City’s leading scorer.
That has not stopped rumours about his future, with Chelsea, Manchester United and Real Madrid all linked with the star, but Khaldoon is adamant Aguero is too important to lose.
“I’ve read a lot about the speculation on this and it is ridiculous,” Khaldoon told City’s website on Tuesday.
“Sergio Aguero is one of the best players in the world and we are a team that aspires to win in every competition we compete in.
“Having Sergio Aguero as part of the squad is an absolute must and has never been a doubt.”
Meanwhile, Benfica goalkeeper Ederson is reportedly due to arrive in Manchester as he closes in on a move to City.
City are still negotiating a settlement on the 23-year-old’s third-party ownership issues, but the club hope he will undergo a medical on Tuesday.
Ederson would become Guardiola’s second close-season signing after Monaco playmaker Bernardo Silva joined on Friday.