Messi could be sidelined until 2014 after suffering his latest hamstring injury during Sunday's Primera Division match at Real Betis, with Barca's medical team estimating he will be out for between six and eight weeks.
Losing the four-time reigning world player of the year is a blow but while Freixa concedes Barca obviously depend on the Argentina ace to a certain extent, they are better placed to deal with his absence now than in previous years.
Freixa, who is the Barca board spokesman and club secretary, said: "The team is always 'Messi-dependent' because it's impossible not to be with the best player in the world. People talk about it like it's something bad but it's a good thing.
"We've improved this weakness now. The team have other resources and it is performing at a great level."
Barca, who signed Brazil forward Neymar in the summer, are still unbeaten under new coach Gerardo Martino this season and boast a three-point lead at the top of La Liga and are also through to the Champions League knockout stages with two games to spare.
Therefore, the prospect of being without Messi for up to eight games - two of which are in Europe and two more are the Copa del Rey last-32 tie with minnows Cartagena - is not such a worrying one.
What will be more of a concern for Barca fans is the hamstring problems Messi has been struggling with, with his latest one being his third of the season.
Freixa has no doubts though that Messi will return as good as before.
He said at a press conference: "We are utterly confident that he'll recover in two months and be the best player in the world.
"If this had to happen it's happened at an extraordinary time, leading the league and qualified in the Champions League, and when the best player in the world gets back we'll be ready to fight for all the titles. Any problems? None."
Freixa also assured that the Barca have total faith in the club's medical staff, saying: "An injury is something that happens in sport. It's a normal injury.
"It's certain that the reason for Messi's injury is that he's been playing at such a high level for so long. That's part of football. We fully expect that his recovery will be satisfactory and he'll be back playing at the highest level as the best player in the world."
Meanwhile, Barca have extended their deal with children's charity Unicef for another two years until 2016.
Barca, who have the Unicef logo on the back of their shirts, said on their website: "The club is committed, as it has done in recent years, to give 1.5million euros each year to joint work with Unicef."
Freixa said: "It's an alliance that we are very satisfied with."