Neuer has been subject to a series of protests from the Bayern supporters, which began even before his move from Bundesliga rivals Schalke had been confirmed.
This culminated in a demonstration during Bayern's recently completed training camp in Italy, but Nerlinger insists that the dissenting group are merely a small, if vocal, minority.
"Ninety-nine per cent of Bayern Munich fans are behind Manuel Neuer," he explained to TZ in an interview.
"You can never rule out the fact that certain people or small groups will want to boost their profile. I am convinced, though, that Bayern's various groups of ultras will soon be unanimous in their support this season."
Former Rangers and Borussia Dortmund player Nerlinger also stated that while the club see strengthening their defence as the key to bouncing back this season, that must not come at the expense of entertaining football.
"After a disappointing previous season, we want to win the title again.
"We want to stabilise our defence and we must be able to once again develop the ability to keep clean sheets. But with the players we have, we cannot play boring football. We have great individuals in attack, along with our attacking potential, we need to be well organised at the back."