Sunday's (AEST) 1-0 defeat at Augsburg was Bayern's first loss of the campaign, but followed three domestic draws against Borussia Monchengladbach, Union Berlin and Stuttgart.
Bayern did win its first two UEFA Champions League group stage games against Inter and Barcelona (both 2-0), but sits fifth in the Bundesliga after seven games.
The club's chief executive Oliver Kahn had already provided his backing to Nagelsmann, saying on Monday (AEST): "We always have the strength to get back to the front, where we belong, to the top of the table."
On Tuesday, Hainer added to that support, saying: "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.
"We are completely convinced of Julian Nagelsmann and our entire team."
Including the end of last season, Bayern has only won three of its last 10 Bundesliga games (D5 L2), though its final three outings of the 2021-2022 campaign came after it had already sewn up a 10th straight title.
Despite that, Hainer said: "After the international break, we will attack again, as we know it from FC Bayern.
"The season has just started and we know we have the potential to achieve our big goals."