Bierhoff also said FIFA's plan to use a number of captains' armbands with different slogans was equally baffling given that Germany and some other European nations would wear their own anti-discrimination 'One Love' armbands to promote inclusion.
For years, Qatar's tournament organisers had said alcohol would be accessible to fans at the tournament, but world soccer's governing body FIFA made a last-minute reversal on Friday, two days before Sunday's kickoff.
The Qatar World Cup is the first to be held in a Muslim country with strict controls on alcohol, the consumption of which is banned in public.
"This is indeed an issue," Bierhoff told a news conference. "It is what I have said also about planning in relation to the captains' armbands.
"Such a short-notice decision (on beer) is unfortunate and creates unease," Bierhoff said.
"This (beer) is a part of the tournament but I cannot really understand the decision and the timing because there was enough time to take such a decision earlier."
Qatar was awarded the World Cup 12 years ago.
Bierhoff said he was equally surprised by FIFA's latest armbands plan, unveiled earlier on Saturday, again criticising the football body's short-notice announcement.
"I heard about that and the short notice is a bit surprising and it's as if FIFA does not have a clear position," Bierhoff said.
"We have a clear position. I will see how this develops and we will discuss with the other nations from Europe. We expect to be allowed to wear the (One Love) armband," he said.
Several nations are planning to wear the armband to send a message against discrimination. Homosexuality is illegal in Qatar.