The Blaugrana great's contract at Camp Nou expired at the end of last season, but he was expected to commit to a new deal ahead of the coming campaign.
Messi reportedly agreed a 50 per cent reduction in wages, with news of the contract anticipated this week ahead of Monday's Joan Gamper Trophy match against Juventus.
But Barca's dire financial situation means they are unable to register new players due to La Liga's salary restrictions.
Messi, like new signings Sergio Aguero, Memphis Depay, Eric Garcia and Emerson Royal, had been left in limbo.
And following widespread reports in the Spanish media, Barca confirmed Messi could not formalise the agreement, meaning he "will not continue to be linked to FC Barcelona".
A statement read: "Despite having reached an agreement between FC Barcelona and Leo Messi and with the clear intention of both parties to sign a new contract today, it will not be possible to formalise it due to economic and structural obstacles (Spanish La Liga regulations)."
"Given this situation, Lionel Messi will not continue to be linked to FC Barcelona.
"Both sides deeply regret that the wishes of both the player and the club cannot ultimately be fulfilled.
"Barca would like to thank the player most sincerely for his contribution to the aggrandisement of the institution and wishes him the best in his personal and professional life."
Messi is widely acknowledged as Barca's greatest ever player, having scored 672 goals and provided 265 assists in 778 appearances.
He has been part of four triumphant Champions League teams, also winning La Liga on 10 occasions.
The 34-year-old finally ended his wait for a first international honour with Argentina at this year's Copa America, but his future is now in serious doubt.
Messi was linked with Manchester City and Paris Saint-Germain when he first pursued a Camp Nou exit last year.
But City appear focused on Jack Grealish and Harry Kane, while PSG have already spent heavily as well as agreeing a new contract with Neymar and opening talks with Kylian Mbappe.
The expectation Messi would remain at Barca leaves no obvious next destination in the immediate aftermath of a shock announcement.
Story published on The World Game, SBS