Thirty people were injured in the early-morning accident, some seriously, while 18 still considered missing "are believed to have died on the burning bus," police said in a statement.
Authorities said that forensic specialists were being brought in from Germany's federal police office to remove and identify the bodies from the charred vehicle. Police spokeswoman Irene Brandenstein said the work was slow and labor intensive given how badly damaged the bus was by the fire.
The highway remained closed on both sides for hours and police tweeted later that the road leading south would be shut down for the entire day.
Several helicopters, firefighters and ambulances were on the scene to rescue the injured.
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Two drivers and 46 passengers were on the bus, Brandenstein said.
Police said that the group on the bus came from Saxony in eastern Germany and that no children were on the bus. The German news agency dpa reported that all passengers were German citizens.
A phone number was activated to provide family members with information. Brandenstein had no immediate information on the condition of the truck driver.
The accident led to long traffic jams on the A9, which is the main thoroughfare from Berlin to Munich.