The toll from enterohemorrhagic E. coli rose to 16 Tuesday when a Swedish woman died after returning from a visit to Germany, the EUobserver reported.
Hamburg health officials said new tests cast doubt on the link to Spanish produce.
At a meeting of European agriculture ministers in Hungary, Germany's Robert Kloos said, "Germany recognizes that the Spanish cucumbers are not the cause."
But Hamburg's health minister stood by the claim.
Spanish Agriculture Minister Rosa Aguilar denounced the German accusation and said the scare had caused heavy losses.
Dr. Rolf Stahl, head of a clinic in Hamburg, told Der Spiegel such an aggressive intestinal bacteria has never been seen.
In the worst cases, EHEC causes hemolytic-uremic syndrome, dissolving red blood cells and triggering kidney failure. The patient's brain is affected too.
"Their awareness becomes blurred, they have problems finding words and they don't quite know where they are," Stahl said.
The syndrome normally afflicts 60 Germans a year, but that many were being diagnosed daily last week. By Tuesday there were 373 confirmed cases.