Six-time Ballon d'Or winner Lionel Messi will leave Barcelona despite both parties having reached an agreement over a new contract, the La Liga club said on Thursday, citing economic and structural obstacles to the renewal of the deal.

Messi, who joined Barca's youth set-up aged 13, is the club's all-time top scorer and appearance maker with 672 goals in 778 games in all competitions.

The Argentina forward was free to negotiate a transfer with other clubs after his deal ran out at the end of June, but Barcelona had always maintained he wanted to stay with the club.

Messi, who has spent his whole career at Barcelona, had been expected to sign a new five-year deal with the Catalan club, which would have included a salary reduction of 50 percent.

Barcelona needed to financially restructure in order to get the deal over the line, which proved impossible in the end as they failed to reduce their wage bill in order and stay within La Liga's Financial Fair Play (FFP) regulations.

La Liga chief Javier Tebas said last month that Barcelona, who have a total debt of more than 1 billion euros ($1.18 billion), would not be shown any leniency when it comes to obeying the league's strict financial control rules. 

The news of Messi's exit comes a day after La Liga agreed in principle to sell 10 percent of a newly formed company housing most of its business to private equity firm CVC Capital Partners for 2.7 billion euros ($3.2 billion). 

"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 La Liga regulations)," Barca said in a statement.

"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."