Bayern are without a permanent head coach following Niko Kovac's sacking, with former assistant Flick in caretaker charge for impressive wins over Olympiacos and Borussia Dortmund.
Manchester City manager Guardiola, Bayern coach from 2013 to 2016, could potentially make an incredible return, according to Sport Bild.
Thomas Tuchel, at Paris Saint-Germain, and Erik ten Hag, at Ajax, have each reiterated their commitment to their current clubs, while the report claims Guardiola "does not seem happy" at City, where he has won back-to-back Premier League titles.
The seemingly unlikely prospect of Guardiola linking up with Bayern again was put to goalkeeper Neuer while on international duty with Germany.
The Bayern stalwart preferred to focus on Flick's fine start, though, saying: "Of course, I can't comment on the rumours.
"We are now here with the national team, I hear [about Guardiola] for the first time. You will see what happens and how those responsible decide.
"At the moment, things are going very well. In the last six days, Hansi Flick has invested everything with his coaching team. We have been very successful twice.
"The people in charge will take a stand [by appointing Guardiola instead] if they want to."
Guardiola won the Bundesliga title in each of his three seasons with Bayern but, having twice triumphed in Europe at Barcelona, failed to deliver the Champions League.
Bayern had been European champions when he arrived in Munich in 2013, replacing Jupp Heynckes.
Neuer was speaking ahead of Germany's Euro 2020 qualifying double-header against Belarus and Northern Ireland, where they will hope to secure their place in next year's finals.
Various scenarios could see Germany through after the first match but Neuer said: "Of course, we want to win the home games and get six points. That's our clear goal."