The Spanish media has been focused on Martino's rotation policy since he substituted star forward Lionel Messi against Real Sociedad in Barcelona's 4-1 win on Tuesday.
It was the second time Martino had taken Messi off before the final whistle in La Liga this season and the four-time Ballon d'Or winner did not look pleased at the Camp Nou.
But Barcelona's head coach does not care what his players think and dismissed any suggestions of a feud.
"I have no disagreements with him nor comparisons with other seasons, this is the first that I am working with him," Martino said.
"Leo does not like being changed nor does Neymar, Xavi (Hernandez), Cesc (Fabregas) and (Andres) Iniesta.
"But I was hired to make decisions that relate to the health of the team and the players over the season, so that they are all fit at the decisive stage of the season.
"I'm going to do that and I am aware that no-one likes to be taken off, I reflect that and understand.
"Traditionally it happens with any player but we are managing the minutes with a view to everything, we cannot divert our attention if we want the full squad in the final stretch."
Barcelona will travel to Almeria on Saturday for their next fixture in Spain's top tier and while the south-coast club are languishing in the relegation zone ahead of the game, Martino has warned his side about their upcoming opponents.
Of the top seven goal scorers so far this season, all but one comes from the top-three clubs; Barcelona, Atletico Madrid and Real Madrid.
That man is Almeria's lead striker Rodri Rios Lozano, who has four goals in six league games this season.
Martino believes if they closed out games, Almeria would be higher up La Liga's standings.
"Almeria missed many points in the end of their games whether one or the three but they do have skilful players especially up front," Martino said.
"Their two wingers are good at one-to-one and also Rodri and Soriano complete well their attacking movements.
"I think every single opponent demands the best from you and to be focused but if we do our game then the chances to win will increase."
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