Guardiola, who joined in 2013 after winning 14 titles in four season at Barcelona and taking a year out, has been a top target for several European clubs.
The Spaniard, who won the domestic double last season, has repeatedly been linked with a possible move to Premier League club Manchester City.
Speculation intensified in the days after Bayern's 3-1 Champions League quarter-final first leg loss at Porto last week and the subsequent departure of their long-time team doctor, who said his medical team was blamed for the defeat.
But their 6-1 demolition of the Portuguese on Tuesday saw Bayern book a semi-final spot with Guardiola on track for a treble of titles in his second season.
"I know very well that he will be the coach here at least until June 30, 2016," Rummenigge told Bild newspaper.
He said contract extension talks would take place in the second half of the year, following the end of the season.
"The aim is to extend Guardiola's contract and I think we have very good chances that he remains the coach here beyond 2016."
Recent contact between Guardiola and former Barcelona colleague Txiki Begiristain, who is now City's sports director, was no reason for concern for Bayern, Rummenigge said.
"I am not worried about that. This just proves the quality of the coach. I am also aware that Begiristain worked with Guardiola at Barcelona at some point."
"But I cannot imagine that Pep would go to a club like Manchester City."
Bayern could win the Bundesliga title this weekend and take on Borussia Dortmund in the German Cup final before their Champions League semi-final next month.
Bayern have once before won the treble, in 2013, shortly before Guardiola's arrival.
(Reporting by Karolos Grohmann; Editing by Amlan Chakraborty)
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