Barcelona goalkeeper Ter Stegen described it as a "massive blow" not to feature for his country against Netherlands and Northern Ireland in the international break.
The 27-year-old has had to serve as back-up to Neuer for most of his international career, despite increasing calls for him to be given the number one spot ahead of the Bayern Munich star.
Neuer accused Ter Stegen of being unhelpful by expressing his frustrations in public and suggested he had shown something of a lack of respect towards Bernd Leno and Kevin Trapp, who likewise are battling for more Germany playing time.
Ter Stegen, who has returned to his homeland for Wednesday's (AEST) UEFA Champions League clash between Barca and Borussia Dortmund, thinks Neuer has been unfair but wants to draw a line under the issue.
He said: "I would like to say something about this. You cannot say we have competition for the goalkeeper position and then expect the players to be happy with the situation if they don't play. Football is about happiness but also disappointment.
"Manuel Neuer does not need to comment on my personal feelings and measure them, I'd say. It's my own opinion. If you think about the last few years, you realise that I always behaved well and what Neuer and other people have said is not fair.
"His remarks were inappropriate but I don't want to say much more. I want to end this controversy."
Ter Stegen's immediate priority is to help sure up Barca's defence, with the Catalans having conceded seven goals in their opening four LaLiga games of 2019-20.
"We're trying to stop the goals going in but things haven't come off," he said. "It's not what we expected. We have to improve. There have been mistakes that we can easily correct. We've spoken about it."