The 33-year-old confessed his comments were ill-timed, but it means he enters a second straight major international tournament with his next move at club level shrouded in mystery.
Ronaldo helped Portugal win Euro 2016 despite rampant speculation over his future and Fernandes insists the captain is paying sole attention to giving his country a second trophy.
"I don't have any kind of negative view. I see him as normal. He doesn't seem to be worried about the future to me," said Fernandes.
"He's very focused on what the national team are doing and being able to help Portugal."
Portugal are likely to be heavily reliant on Ronaldo for success in Russia, but Fernandes insists that is only natural when you have a five-time Ballon d'Or winner in the squad.
"Given that he is such an important player for the team and one of the best in the world, it is normal that we have some dependence on him," he said.
"It's perfectly normal, however Portugal were the champions of Europe because of the group, not its individuals.
"In no way can Cristiano Ronaldo be detrimental to our team. It would not make much sense. He's very demanding with himself and ends up demanding a lot from us as well."
First up for the European champions in Russia will be Iberian rivals Spain, one of the leading contenders, in Sochi on Friday.
Fernandes highlighted Andres Iniesta as one of their key components, but he is content the talent at Portugal's disposal is sufficient.
"I'm a fan of Iniesta, but I don't want any players from Spain," said the Lokomotiv Moscow midfielder. "They have a lot of respect for our team and will always play in the same way.