Although Bayern are third in a very tight Bundesliga after eight games, they are enduring their worst start to a league campaign since 2010.
Kovac's side won 3-2 against Olympiacos during midweek in the Champions League but the defensive issues that have plagued their campaign were on show throughout in Greece.
Bayern have kept just two clean sheets all season and the knocks picked up by Javi Martinez and Lucas Hernandez in that game will provide encouragement for Union Berlin, who have, on average, fielded Europe's tallest starting XI this season.
The centre of attention for the Bavarian giants on Saturday in the first ever competitive meeting between the two clubs will be Polish striker Robert Lewandowski, who will become the first player to score in the opening nine games of a Bundesliga season if he adds to his tally of 12 from the opening eight matchdays.
Fischer's team won last weekend against Freiburg to secure their second victory of the season and end a four game losing run.
Die Eisemen have acquitted themselves fairly well since entering the Bundesliga, playing around with their formations but mostly sticking to the same basic approach.
Berlin usually field three central defenders with wing backs providing attacking outlets in the wide channels, with those players then dropping back when they are out of possession to create a back five.
However, Fischer's side have often been undone by their indiscipline this season, incurring three red cards in their opening eight games, and they will need their full complement to keep Bayern quiet at the Allianz Arena.
Bayern Munich recent form: WWDWLD
Bayern Munich recent form (all competitions): WWWLDW
Union Berlin recent form: WLLLLW
Aside from that Kovac has a mostly fit squad to choose from for Saturday's game and the Croat is likely to rotate some players, with Leon Goretzka and Ivan Perisic among those potentially set to be offered starting berths.
The Bayern coach's main decision will be whether to start Lewandowski or bring him on from the bench during the game in order to give him some rest ahead of a key run of fixtures for the Bavarian side.
Fischer is likely to field a similar side to that which beat Freiburg last weekend, although he may elect to go with a 3-5-2 that better accommodates their big Nigerian striker Anthony Ujah.
Bayern Munich possible starting lineup:
Neuer; Kimmich, Pavard, Boateng, Alaba; Tolisso, Thiago; Coman, Goretzka, Perisic; Lewandowski
Union Berlin possible starting lineup:
Gikiewicz; Friedrich, Schlotterbeck, Parensen; Bulter, Gentner, Schmeidebach, Andrich, Lenz; Ingvartsen, Ujah
We say: Bayern Munich 3-1 Union Berlin
Although Union Berlin may be able to exploit Bayern's recent defensive frailties with an early goal, the home side should have more than enough to get back to winning ways in the Bundesliga.