Messi, who was only making his third appearance after missing three weeks with a thigh injury, looked below his best and lacked the confidence in sprints against Barca's traditional rivals. (Agencies)
That had prompted comments that the little Argentinean is not in good physical condition, but Martino rejected the assumption, media reported.
"The worries about Messi come from outside of the club and not from inside. I am not worried if he scores or fails to score goals, because what he gives the team is always vitally important," he commented, before explaining why he had made Messi play on the wing against Madrid.
"We spoke to him at the start of the season and I commented that it was good to be able to use him in different places as we think he can unbalance things more from there. There are times when we will use him as a striker, or in a deep role, but we want to have him at his best so we can use him where he is needed," said Martino.
The coach has decided to rest defender Gerard Pique ahead of Tuesday's game against Celta Vigo, explaining "we thought in the rotations that it was better if Gerard didn't play".
As expected, Martino was asked about the Clasico and gave his version of events in a match in which both sides saw refereeing decisions going against them, with Madrid claiming a penalty for a push on Cristiano Ronaldo, while Barca believed Madrid's Sergio Ramos should have been sent off, while asking for their own penalty after an apparent foul on Cesc Fabrigas by Pepe.
"There probably was a refereeing error, but they also played the game and you have to think about that. Barca were better in the first half, Madrid were better in the first 25 minutes of the second half and then it was pretty even," he said, warning of the danger that after being their historic rivals, Barca could take their eye off the ball in Vigo.
"There is always that risk after playing a Clasico, but there is no place to start feeling comfortable," commented Martino, who assured he was "delighted" with the current situation of his team which have taken 28 points from a possible 30 at the start of the season.
Finally Martino insisted Barca were favourites to win the title.
"We were favourites when we beat Levante in the first game of the season, also after the fifth and the tenth games. We are favourites in whatever we play because that is what our category and history dictates," he concluded.
Messi, who was only making his third appearance after missing three weeks with a thigh injury, looked below his best and lacked the confidence in sprints against Barca's traditional rivals.