Bayern had repeatedly claimed it had no intention of letting players such as Thomas Mueller, Mario Goetze and Javi Martinez leave, saying everyone was needed at last season's treble winners.
Last week, Guardiola himself said he was certain the trio would stay at the club next season despite speculation that suggested they could be eyeing transfers to secure first-team action.
"If a player does not feel well at Bayern Munich then he needs to come to my office," Rummenigge told Bild newspaper on Monday. "We must then talk about it."
Home-grown talent Mueller, an automatic starter in previous campaigns, has cut an unhappy figure on the bench in Guardiola's first season in charge with a possible move to the English Premier League widely reported.
Mueller said he was "certainly not happy" after being on the bench for their Champions League semi-final first leg at Real Madrid a few weeks ago.
Midfielder Toni Kroos has also been linked with a move to Manchester United.
The 24-year-old Mueller refused to talk about a possible departure from the club where he has played for since his youth, telling reporters on Saturday that he had "no comment, no comment", before rushing off.
(Reporting by Karolos Grohmann; Editing by John O'Brien)
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