He argued that forcing the German national team to play nations such as Albania and Moldova was a slight.
Beckenbauer, a former World Cup winning manager of Germany, called on the governing body of European football, Uefa, to end "these stupid games" and said smaller countries should play separate qualifiers in international competitions, allowing the "great" football nations to play against each other.
"Our team should only play major nations like Italy, England or Holland," the Bayern Munich chairman wrote in Germany daily newspaper Bild. "But at the moment we have to wait two years before we meet these football greats.
"That's why games against countries like Moldova are a slight to the German national squad. They're just stupid."
Germany defeated Moldova 3-0 on Wednesday and face Albania in Kaiserslautern tomorrow in the European Championships.
"Moldova, Albania, or whatever all these countries are called, should first play qualifiers and only later face the football greats," Beckenbauer wrote.
He complained that there were now so many countries competing in international competitions that qualifying groups were "almost totally made up of exotic teams".
"Sure, we have to help these countries. We should be sending them money but please, don't let them play for points in the European Championships."
Beckenbauer, who inspired Bayern to three European Cup wins in the mid-1970s as well captaining Germany to a World Cup triumph in 1974, has not hesitated to raise controversial issues recently. The world governing body, Fifa, told him last month to stop complaining about the rules after Beckenbauer described them as stupid.
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