Politicians, human rights campaigners and their own fans have all criticised the Bavarians for choosing Qatar which has been widely criticised for its treatment of migrant workers.
The Bundesliga champions and current leaders were visiting Qatar, one of the wealthiest countries in the world which is preparing to host the FIFA World Cup in 2022, for the sixth year in a row.
"Apparently, nothing has been learned. Bayern are travelling to Qatar again, as if there were no other countries in the whole world for a training camp," tweeted Ozcan Mutlu, a Green Party member of the Bundestag lower house of parliament.
Last year, Bayern, one of the world's biggest clubs and a leading global football brand, also made a one-day trip to Saudi Arabia to play a friendly game organised by a club sponsor.
That trip coincided with the uproar over the flogging in the country of activist and blogger Raif Badawi and Bayern later apologised for failing to voice their support for him.
Wenzel Michalski, Germany director of Human Rights Watch, said Bayern could not turn a blind eye to the situation in Qatar.
"When football clubs train in Qatar or Dubai, they must address the human rights situation," he said on Twitter.
Bayern's own fans have also criticised the trip and one, Yalcin Imre, said he was cancelling his membership of the club.
Imre said in a post on Facebook that there were other issues which also came into play, but the choice of Qatar was the final straw.
"The decision for a new winter training camp in Qatar.... made the barrel overflow as far as I am concerned," he said on his Facebook page. "There are plenty of good alternatives around the world, where human rights are respected."
The Qatari government has denied that workers are being exploited and said that Qatar has made reforms including a wage protection system requiring companies to pay salaried workers by electronic bank transfer and a law making it illegal for companies to withhold workers’ passports.
Bayern captain Philipp Lahm, clearly choosing his words carefully, told reporters at Munich airport that the Bayern players were not oblivious to the situation.
"The whole team are all occupied with the subject of what's going on in Qatar," he said. "We have not closed our eyes."
Chief executive Karl-Heinz Rummenigge said late last year that the decision to choose Qatar was "not a political statement."
(Writing by Brian Homewood in Berne, editing by Pritha Sarkar)
