Bayern faced protests from their own fans at a home match last year when supporters displayed banners which read 'money (over) human rights', 'capital (over) morals' and 'open your eyes when it comes to sponsor choice'.
Qatar, which will host the 2022 FIFA World Cup, has faced several allegations of migrant worker abuse from human rights organisations including Amnesty International.
In particular, it has been criticised for the work-sponsorship system known as 'Kefala' which requires all foreign workers to obtain their employer’s consent to travel abroad.
In September, Qatar said it would end the exit permit system in move described as a 'significant step' by the International Labour Organisation.
Rummenigge said Bayern were one of many German companies involved in business with Qatar, which he said had been responsive to criticism.
"Like other football clubs and sports associations, we are also engaged in a dialogue in the Gulf region," he said in an interview with the Munich-based daily Abendzeitung.
Rummenigge said Bayern had regular exchanges with their partners in Qatar 'including the issue of human rights and the rights of workers'.
He added: "International trade unions and NGOs have agreed that Qatar has responded to public criticism and made changes, including the positive development of the legal status of migrant workers and improvements in Qatar's labour rights."
Bayern first held their training camp in Qatar in 2011, saying at the time it had perfect conditions for a winter break.
The club subsequently strengthened their ties by signing a sponsorship deal with Doha airport and in July last year Qatar Airways became one of their partners.
Bayern are Germany's most successful football club and have won the Bundesliga for the last six seasons, although they went into the winter break in second place, trailing six points behind leaders Borussia Dortmund.
