The six-time Ballon d'Or winner is reportedly looking to leave the Camp Nou after growing frustrated with club's board and president Josep Maria Bartomeu.
Reports in Spain claim Messi's decision is final, but Calderon feels the competition between the two El Clasico outfits could be affected if the Argentine does end up leaving.
"It is important to have a team like Barcelona in our league, and for Real Madrid as well to have as a rival. It makes both teams better," he told Stats Perform News, as per Goal.
"It used to happen with Cristiano [Ronaldo] and [Lionel] Messi. The fact that both have been in those teams made them better players. It encouraged them to improve themselves and win more trophies in order to beat the other. It is the same with Real Madrid and Barcelona.
"The clubs are always in a competition. This is what should happen between those two clubs.
"This time is not good for Barcelona, that's clear. So, what is not good for the rival, in theory is good for the other - but I don't like it. I never liked it when it happens to any team.
"I have always said Barcelona is a very big team. It is not an enemy. I have always had a great relationship with the presidents and the board I met.
"I was always well-treated there and I tried to do the same with the ones who came to our stadium. It is clear Barcelona is in a tough time, but hopefully they will overcome it.
"It is not good to have such a big team [in a situation] like this and I am sure they will overcome the situation. Even if it is good for Real Madrid in some aspects, I don't like it.
"I wish them to fix it and keep giving glory to Spanish football. I wish them to keep competing and winning titles, when they don't face Real Madrid, obviously."