N'Zogbia looks set to return to action for the visit of Sunderland to the DW Stadium on Saturday having been left out of the squad for the Latics' last game, a 1-0 win at Tottenham played three days before the August 31 transfer deadline.
At that point the Frenchman's future appeared uncertain after Wigan had reluctantly agreed a fee for him to move to Birmingham, only for the deal to collapse when N'Zogbia altered his demands.
However, Martinez has since been impressed with the 24-year-old's attitude in training and is ready to consider him again for first-team selection this weekend.
The manager claims retaining N'Zogbia is akin to bringing in a new transfer - but as far as actual trading is concerned, Martinez believes it is "not healthy" the window should stay open after the Barclays Premier League season has started.
Asked if N'Zogbia was in his thoughts for the Sunderland game, Martinez said: "He is, but not just because I'm saying it. It is the way he has been working in the last five sessions.
"I don't blame Charles, I just blame the situation. I think the authorities in football should really look into it and we should help the players on the human side, to help them focus on concentrating on their jobs.
"Having the transfer window open while competition is going on is not healthy - it doesn't help anyone, not just Wigan Athletic.
"I think you could go in every single dressing room in the Premier League and in a different manner, everyone has been affected.
"It is important that the players have time to think about their futures and the next step for their families, and there is a period to do that in the transfer window.
"But it shouldn't be while competition is going on - it is disrespectful to the fans and devalues the league as a whole. We should close the window before the first game starts.
"But I have been delighted with Charles' attitude. He looks focused and concentrated.
"He made the final decision to stay - it wasn't imposed on him at all, so we have signed a new player."
With the window now shut, Martinez is confident both N'Zogbia and Wigan can move on.
"I feel that whatever the thoughts were and whatever the different options were that he had to consider, that is well in the past," the Spaniard said.
"Now he is ready, he is focused and all he wants to do is help Wigan Athletic to carry on being competitive.
"From his position, he is ready to show everyone that he wants to enjoy his football with us."
Another player who missed the victory at White Hart Lane was goalkeeper Chris Kirkland, who had conceded 10 goals in Wigan's opening two games this season.
Ali Al Habsi performed well in his absence but Martinez stressed afterwards Kirkland did not play due to a hip problem and today confirmed having returned to full fitness, the former Liverpool stopper would be back in the squad on Saturday.
"Chris is fully fit. He is 100%, has trained really well in the last five sessions and he is going to come straight into the squad," Martinez said.
"I am probably now in the best position since I arrived here in terms of goalkeeping options, and to have someone like Ali performing in the manner that he has and then having Chris fit, that is a very strong position to be in.
"The hardest thing in life and football is to earn respect and I think Chris has done that with the performances he has had over the last few seasons.
"Sometimes he has played through the pain barrier and he has done it for the football club.
"That will always be in my mind, so whether Chris is in a good or bad moment of form, he will always be an important player for Wigan Athletic and will be straight into the squad on Saturday."