The midfielder, 27, has been linked with a big-money switch to Old Trafford in a bid to boost the Red Devils' chances of winning the Premier League this season.
However, Bayern CEO Karl-Heinz Rummenigge has rubbished speculation linking Thiago with a move away.
He told Abendzeitung: “Thiago is an important player for us and we have never once articulated the thought that he should leave the club.
“There has never been anything to the story whatsoever.”
New Bayern boss Niko Kovac has also expressed his hope that Thiago will remain at Bayern, though he said he could not offer a “guarantee”.
Kovac said: “I first want to get to know him. I hope and believe that he will play for Bayern [this season].
“But I can't give a guarantee. We have to wait until the end of August.”
Goal reported earlier this month that Man City had ruled out making a move for Thiago this summer.
It would have seen Thiago link up again with Guardiola, with the pair having worked together at Barcelona, but the English champions are not aiming to sign the Bayern man.