Argentine superstar Messi has not played since suffering a hamstring tear against Real Betis on November 10.
However, he returned to training earlier this week and is on course to feature when Barca travel to Madrid next week for a top-of-the-table La Liga clash.
"I sincerely believe that Lionel Messi will be fit for the Atletico Madrid fixture. But I am not going to play anyone who is not fully recovered from an injury," Martino said after Sunday's 4-0 home win over Elche.
"I won't modify this principle depending on the team we face."
"We know how important the game against Atletico is," added the 51-year-old.
"Regardless of what Simeone says, Atletico is in top form, has great players and is one of the main contenders for La Liga and Champions League titles.
"If you were a spy inside Atletico Madrid's locker room you would heard that they have great expectations for this season.
"It's fine that Barcelona and Real Madrid have all the pressure, but Atletico can achieve great things.
"However, the fact that we play against Atletico won't change our principle of starting those who are fit."
Messi could yet feature in Wednesday's Copa del Rey tie against Getafe.
"As I said, Messi is really well," added Martino.
"We have to talk to each other to see how he feels because he has to get over his mentality too; he has to feel ready 100 per cent.
"I think now that is the most important because maybe he is now a bit afraid of getting another injury and once he gets over that he will start to play."
