"Surgery was necessary to treat an inflammation caused by operation scars," the club said in a statement, referring to the first time he went under the knife in December.
"His recovery will only be slightly delayed. He can resume his rehabilitation after 10 days."
Badstuber tore cruciate ligaments in a 1-1 draw against champions Borussia Dortmund at the end of 2012.
The Germany international, who has been plagued by injuries this season, said in January he hoped to be back before the campaign ended.
Bayern are 17 points clear at the top of the Bundesliga and through to the German Cup semi-finals.
They also face Arsenal next week for a spot in the Champions League last eight, having won the first leg in London 3-1.
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