The club legend, who has spent his entire senior career at the Nou Camp, will not sign a new deal with the club due to La Liga restrictions.
The Spanish league want Barcelona to shave off almost £200m from their wage budget this summer, which they have been unable to do.
Laporta, who has previously vowed to keep Messi at Barcelona, held a press conference today to give his side.
“I’m here to explain the situation we have reached in negotiations with Lionel Messi,” he announced as he began speaking to the media.
“The inheritance we received has been awful. The losses are higher than we expected and what we are spending is a lot more than we expected.
“Our salary mass is not leaving any margin. Financial Fair Play is also blocking us. I can’t make a decision that could destroy the club, Barça are the most important thing.
“I am not willing to mortgage Barça’s television rights for half a century. Our institution has 122 years of history and is above any player, even the best in history like Messi, to whom we will be eternally grateful. Above players, managers and presidents, Barça will always be above them.
“Making an investment of the characteristics of this one was risky. We were willing, but when we knew in depth the economic health of the club we didn’t want to put Barça’s stability at risk.
Messi wanted to stay at Barça. So did we. The will was clear. I am grateful to those who have negotiated both on the part of the club and Messi’s representatives.
“Different aspects had to be made compatible, the interests of both parties, to comply with the FFP. The player has other proposals. In a negotiation you have to stand up and you have to leave emotions aside and work with rigour and coolness.”
Barcelona confirmed the monumental news on Thursday evening, hours after reports began circulating that Messi would not be renewing.
A club 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 cannot be formalized due to economic and structural obstacles (Spanish LaLiga regulations).
“Given this situation, Lionel Messi will not continue linked to FC Barcelona. Both parties deeply regret that the wishes of both the player and the Club cannot finally be fulfilled.
“Barça would like to thank with all its heart the player’s contribution to the enhancement of the institution and wishes him the best in his personal and professional life.”
The situation has left Messi distraught according to a report by Diario SPORT.
The Argentinian had agreed a five-year extension, with a 50 per cent pay cut – which was set to see him pocket €20m-a-year.
Barca fans took to the streets outside the club’s headquarters last night in protest at the loss of their talisman, with some devastated supporters seen in floods of tears outside the Nou Camp Stadium.