Mandzukic left Wolfsburg for Bayern in 2012 and he still has a further two years to run on his contract at the Allianz Arena.
However, the impending arrival of Robert Lewandowski from Borussia Dortmund at the end of the season has placed a question mark over Mandzukic's future with the European champions.
Franz Beckenbauer conceded in January that the 27-year-old could leave, but Allofs has cast doubt on the prospect of the Croatia international returning to Wolfsburg.
"A transfer for Mario Mandzukic is unlikely," Allofs told SPORT1 media after the forward scored twice in Bayern's 6-1 win at Wolfsburg last weekend.
"We will be able to just do a few things and we won't be able to pay every transfer fee. Of course, we have a good squad and we want to get better.
"It's a fact we are trying to find a striker that is able to help us a lot up front, there is no doubt about it."
Pierre-Michel Lasogga is another striker who has been linked with a move to Wolfsburg, but Allofs has dismissed the latest speculation concerning the 22-year-old.
Allofs added: "I have already ruled it out three times. Apparently, these statements just force other questions in this respect. To point it out for the last time - no!"
Lasogga, who previously had a spell with Wolfsburg's youth team, is currently on loan at Hamburg from Hertha Berlin, where he has a further season left on his contract.