Messi’s contract with the Blaugrana giants expired at the end of June but he was expected to sign a new five-year contract which would have seen his salary reduce by 50 percent.
However, Barcelona are still reeling from financial complications arising from the coronavirus pandemic and have been unable to put a suitable package together to retain their influential skipper.
A statement on the club's website read: "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."
Messi made 778 appearances for Barcelona after making his debut in 2003 and is the club’s all-time top scorer with 672 goals. He won 35 trophies with the club including four UEFA Champions League trophies and 10 La Liga titles.