Messi joined Paris Saint-Germain earlier this summer after Barca failed to offer him a new deal owing to their financial difficulties all throughout the transfer window. But Tebas has claimed the situation could have been avoided.
He told Sport: "Just like when Cristiano Ronaldo, Pep Guardiola or Jose Mourinho left. We knew that one day this would happen. We have had the great luck of having the two best footballers in the world in the two best teams in the world and from La Liga we have been able to take advantage of this to put ourselves on the world front line.
"Perhaps Messi's departure has been a bit more painful, because personally I consider him the best in history, and he didn't deserve to leave like that, not only for Barça but for La Liga as well.
"I discussed it with [Barcelona president Joan] Laporta personally, by phone, and with his board of directors. Solutions were sought, if the reason was economic. If it has been for another reason, I can no longer value it.
"I think that next season, with the numbers that Barca release, we will see if Messi could really have stayed or not. And although I respect the decision of the club, you have to tell things as they are. It was not an economic decision. I know for sure."
Tebas also spoke about Financial Fair Play and whether the UEFA have been too lax on clubs like PSG and Manchester City. He added: "The problem with FFP currently is it's always applied a posteriori. On this issue, we must remember both clubs were sanctioned by UEFA follow LaLiga's complaints, and the CAS absolved them. And there is the problem.
"As in the case with Barça, who have had to act beforehand, and I can guarantee that's helped them beat the crisis. But it's clear that what PSG do is intolerable, the same as City and other clubs. I repeat, it's intolerable, it's (financial) doping."