The German centre-back is out of contract at Chelsea in the summer, and has shown no inclination to sign a new deal.
According to Goal.com, Bayern contacted Rudiger's agent and brother Sahr Senesie regarding a free transfer move in the summer.
"I'm not a fan of talking about players under contract at other clubs, and we're outside the transfer period," Naglesmann told a press conference.
"He's a German international, and is performing very well.
"Thomas [Tuchel - Chelsea coach] helped him reach his best level."
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