The club’s all-time leading goalscorer, 34, is leaving because they could not afford to give him a new contract under La Liga’s salary limit.
A private equity firm wanted to invest in La Liga, which could have made signing Messi possible, but would have meant Barca giving up some TV rights.
“I can’t make a decision that will affect the club for 50 years,” he said.
“The club is over 100 years old and it’s above everyone and everything, even above the best player of the world. We will always thank him for everything he’s done for us.
“In order to have fair play, we need to do this or make an effort which would put the club at risk. We couldn’t keep going with this and we needed to make a decision, which we have.”
Messi had agreed a new five-year contract on reduced wages – but the club still had to slash their wage bill to afford him, and were unable to do so.
“Leo wanted to stay, so he’s not happy. We all wanted him to stay. For him, he has to confront reality. It’s a reality that can’t be changed and he knows I wish him the best wherever he goes,” he said.
Messi – who is being strongly linked to Paris St-Germain – is Barcelona’s record scorer with 672 goals and has won 10 La Liga titles, four Champions Leagues and the Copa del Rey seven times, as well as claiming the Ballon d’Or on a record six occasions.
Private equity firm CVC wanted to invest 2.7bn euros into La Liga in exchange for 10% revenue and a 10% stake in most of its business, but Barca – who felt it would affect future TV deals – and Real Madrid opposed the deal.
“The only way to have that salary margin now was to accept the operation we don’t think is interesting for Barcelona,” Laporta said.
“It’s an operation that puts at risk the club for the next 50 years. We can’t do that.”
He added that he did not want to give “false hope” on “hypothetical” ideas that would see keeping Messi possible.
“Leo’s legacy is excellent. He’s made history,” he said. “He’s the player with the most success in history of the club. He’s been the reference of an era which has been splendid. The best era of Barca’s history until today. A new era starts now. There will be a before and after Leo.”
Laporta, who became president in March after Josep Maria Bartomeu stepped down in October – says a recent audit shows the club’s financial situation is worse than they expected – and that he initially thought La Liga would allow their new contract with Messi.
“We haven’t had six months [to sort this out]. We’ve had less because the audit numbers have just come out,” he said. “The initial figures, we’ve realised the situation is even worse than expected.
“We’ve gone from bad to worse.
“The first offer was two years of salary to be paid in five,” Laporta said. “When we thought that would be allowed in FFP, the criteria of cash came into play. It’s not allowed here, while it is in other countries. La Liga had its pressures because other clubs want the regulations and rules to be abided by.
“Then we agreed a five-year contract. We thought that would be allowed by FFP regulations, and I had insinuated in a convincing way this would be allowed, but after a technical analysis by the La Liga commission. we found out it wouldn’t be valid within those regulations.”