The country's football league body (DFL) has attempted to implement a safer stadium experience into stadia, but the Bavarians supremo would permit flares if the correct security measures were in order.
"Of course, flares look great, but [to use them] we need a security policy," he was quoted as saying by Bild.
"I will allow pyrotechnics once there is legislation. Everyone knows that I am a big pyromaniac."
However, Bayern CEO Karl-Heinz Rummenigge is strongly against the idea of pyrotechnics, citing excessive fines and club tradition.
"There are three things that Bayern don't accept - violence, racism and pyrotechnics.
"Bayern have had to pay out €130,000 in fines for ultras offences over the past year. That's enough!"
The German Explosives Act condemns the unauthorised burning of pyrotechnics, amid concerns over fan safety.
"The highest safety standards are not compatible with the use of pyrotechnics in stadia because there is no room," German Football Federation (DFB) security chief Hendrik Lefert explained.
In November, a fan protest at Hamburg's Imtech Arena over the use of flares at football matches in Germany backfired when several banners caught fire and five supporters suffered burns.