The payment by Bayern was made and repaid in 2003 after heavy investment by the Dortmund board had put the club into dire financial straits and the loan was accepted by then president Gerd Niebaum and manager Michael Meier.
In March 2005, the club was again in financial trouble and on the verge of bankruptcy as they only just managed to avoid insolvency, but corrected their cash situation enough to become German champions last season.
"When they couldn't pay up anymore, sometimes even for salaries, we gave them an unsecured loan for a few months," revealed Bayern president Hoeneß. "I'm a big fan of tradition in sport and I don't think that was a bad thing to do."
Dortmund's chief executive officer Hans-Joachim Watzke has confirmed the Bayern loan to regional newspaper the Ruhr Nachrichten.
Bayern coach Jupp Heynckes has said he does not believe Hoeneß' comments are planned to unsettle their Dortmund rivals who are top of the league on 43 points with Bayern in second place on 41 points and level with Schalke 04.
"I do not see this as calculated," said Heynckes on Monday at a press conference.
"It was a good few years ago and I think it is a positive thing there is some solidarity in the league."
Dortmund have since turned their finances around and managed to sign Borussia Mönchengladbach's rising star Marco Reus for €17.5 million to play for them next season, having seen off competition from Bayern.