Argentine Aguero also explained that he has suffered from a knee injury since 2013 but that surgery has left him “feeling like new” ahead of the World Cup.
He is set to join forces with Messi in Russia, where Argentina will be among the favourites despite a 6-1 hammering by Spain in March.
Despite their friendship, Aguero dismissed any likelihood they might one day wear the same club colours.
“I think it’s impossible,” Aguero told Argentinian television channel TyC Sports on Thursday.
“Before there were possibilities but we are now at an age where Leo is going to end up being at Barcelona and for now, I will end up staying at City.”
Aguero scored 21 goals for City in the Premier League this season despite it being cut short after he aggravated an injury to his right knee.
The 29-year-old planned to put off surgery while City remained in the Champions League but when they were knocked out by Liverpool, his thoughts turned to the World Cup.
“After five years, I feel like new in my knee,” Aguero said, having undergone an operation in April.
“The truth is that since 2013 I have been suffering with my knee – that season I had problems, after 2014 I had problems – something always bothered me in the knee.
“I spoke with the Manchester City doctors this season and said, ‘we are going to wait because we have the Champions League’. But it did not improve.
“Pep supported me a lot, told me to stay calm and after we lost in the Champions League I talked to the doctors and told them I did not feel well. I said I preferred to do surgery because I could have missed the World Cup.”
On his fitness for the upcoming tournament, Aguero added: “I am fit, and I will arrive more rested than many others.”