Whelan downplayed reports linking the Spaniard with another Premier League side this summer, but acknowledged that the former Swansea City coach could one day move on to a bigger team.
"I've always said to Roberto he will go to a big club in Europe or the Premier League," Whelan told talkSPORT.
"When that time comes he will approach me and I will release him and I will give him my very best wishes and thank him for what he has done for Wigan Athletic.
"Until that day comes he is the manager of Wigan Athletic and one of my great friends. He gets on very well with me, he gets on with the players and the crowd love him.
"So over this coming six to twelve months or in two years I will expect him to go to a top club."
Martinez was linked with a move to Aston Villa last season, but opted to remain with Wigan after keeping them in the Premier League.