The cucumbers were infected with a severe complication of E.coli called hemolytic-uremic syndrome (HUS), however, it's unclear whether the cucumbers were infected at the source or during transportation.
Hundreds of people are said to have fallen sick, most of the cases are around Hamburg.
The officials in the Czech Republic said the cucumbers may have been exported there, as well as to Austria, Hungary and Luxembourg.
Czech authorities said the European Union's rapid warning system had told them of an import of the cucumbers into the Czech Republic.
The aggressive form of E.coli is known to cause kidney failure and affect the central nervous system.
The Sweden-based European Centre for Disease Prevention and Control said the outbreak was one of the largest described of HUS worldwide and the largest ever reported in Germany.
It said, While HUS cases are usually observed in children under five years of age, in this outbreak 87% are adults, with a clear predominance of women (68%), the report stated.
HUS cases have also been reported in Sweden, Denmark, the Netherlands and the UK - linked to German travel.
A scientist from Munster University, Helge Karch, warned that the spread of infection was not over. It is possible that there will be secondary infections during this outbreak as well. These secondary infections work from man to man and they can be avoided. That's why we have to do everything possible for better personal hygiene, he said.
Czech Agriculture and Food Inspection Authority spokesman Michal Spacil told AFP that the cucumbers were also distributed to Hungary, Austria and Luxembourg. Spain has announced restrictions on two suspected exporters, the report added.