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The Argentina international left Manchester City at the end of last season and signed for Barcelona as a free agent in July.
Aguero is close friends with the six-time Ballon d'Or winner and publicly spoke about playing with him at club level.
La Porteria reports Aguero's 'future at Barca does not look good' after being promised Messi's new contract had been sorted.
At his official unveiling Aguero said: "Of course I hope to play with Lionel. I know him so well, we're good friends.
"What happens with Leo is a decision that he and the club will make. It is a pride to play with him. I've played with him in the national team."
Barcelona signed Memphis Depay and Eric Garcia this summer alongside Aguero but none of the trio are officially registered yet.
Barcelona are unable to register any new players due to their inflated wage bill not fitting in La Liga rules.
Messi became a free agent in July and agreed terms on a new contract, but has been denied signing it.
The club said in a statement: "Despite FC Barcelona and Lionel Messi having reached an agreement and the clear intention of both parties to sign a new contract today, this cannot happen because of financial and structural obstacles (Spanish Liga regulations).
"As a result of this situation, Messi shall not be staying on at FC Barcelona. Both parties deeply regret that the wishes of the player and the club will ultimately not be fulfilled.
"FC Barcelona wholeheartedly expresses its gratitude to the player for his contribution to the aggrandisement of the club and wishes him all the very best for the future in his personal and professional life."
The Blaugrana have attempted to offload players this summer but it hasn't worked out.
French giants Paris Saint-Germain are in pole position to sign Messi with Neymar, a former teammate of Messi's, playing a key role in convincing the forward.
Barcelona finished third in La Liga last year, behind Real Madrid and title winners Atletico Madrid.
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