The 26-year-old forward and four-time Ballon d'Or winner was ruled out for the rest of 2013 after tearing his hamstring in Barca's 4-1 win over Real Betis last month.
The Catalan club have slipped to consecutive defeats in Messi's absence, losing 2-1 to Ajax in the Champions League before seeing their unbeaten record in La Liga ended by Athletic Bilbao last Sunday.
Argentina international Messi is currently recuperating in his homeland and Martino insists the player will not be rushed back into action, casting doubt over whether he will be fit when Barca clash with Atletico on January 11.
"He is working as planned, completing the different stages of his recovery," Martino said.
"We hope that he will be ready at the start of January, but the closer we get to the date we will see if he needs more time.
"We cannot guarantee when he will be ready; what interests us more is that he has completely recovered."
Barca have been widely criticised following their back-to-back losses but Martino believes the recent setbacks have not affected morale in the camp.
"There are two options, that the pessimism harms us or makes us even stronger," he added.
"We are full of optimism. We need to transform that into the matches. We need to show that we are going to fight and there is a reason why we are top of the league and in the Champions League last 16.
"I don't want to say that we are not worried by losing two games, but we are not loaded by pessimism."