Bayern have failed to win in their past four league games, slipping to fifth on the table after going down 1-0 to Augsburg on Saturday.
The 35-year-old head coach had led Bayern to the Bundesliga title last term in his maiden season in charge, while they have two wins from two Champions League games this campaign too.
Despite that, there has been pressure on Nagelsmann, given their results along with talk of disharmony within the playing group.
Hainer moved to shut down that speculation, insisting that Nagelsmann’s job was not under threat.
“We are completely convinced of Julian Nagelsmann and our whole team,” Hainer told TZ Munich.
“After the international break we will go all-out again, as you know FC Bayern.”
He added: “Four Bundesliga games without a win at Bayern is, of course, not what our fans and all of us imagine.
“We see the multitude of goal chances that our team creates in every match and that are currently not reflected in our results.”
Bayern CEO Oliver Kahn had already publicly offered his support to Nagelsmann.