The six-time Ballon d’Or winner has officially been a free agent since July 1 after he failed to agree terms over a renewal before his previous Barcelona contract expired on June 30.
However, the 34-year-old had been expected to sign a new five-year contract with the Catalan club, which would have seen his salary reduced by 50 per cent.
In a statement, the club said: “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 has spent his entire career at Barcelona, coming through the club’s academy before going on to score 672 goals in 778 appearances after making his senior debut in 2003.