It had initially offered 150m euros, but EU Farm Commissioner Dacian Ciolos raised the figure after coming under pressure from major producers.
The offer is still a fraction of farmers' estimates of their losses, which go as high as 417m euros a week.
The outbreak has so far left at least 26 dead and infected 2,400.
Cases of the rare strain of enterohaemorrhagic E. coli (EHEC) have been concentrated in the northern German city of Hamburg.
Germany's health minister has said infections are dropping significantly, though he warned that more deaths were expected.
Health authorities in Germany erroneously blamed Spanish cucumbers, before an organic bean sprout farm in northern Germany came under suspicion.
Some samples from the farm have tested negative, with results of other tests still pending.
Scientists and German officials have warned that the origin of the infection might never be found.
'Deep crisis'The compensation offered by the EU covers the period from the beginning of the outbreak late last month until the end of June.
Continue reading the main story Spain: 200mItaly: 100mNetherlands: 50mGermany: 30mFrance: 30mBelgium: 6mDenmark: 750,000Lithuania: 150,000Source: European farmers' union Copa-Cogeca
"We don't know how things are going to evolve. We cannot predict," Mr Ciolos said. "At the end of June we will see where we stand."Producers of fruit and vegetables have lobbied to be compensated in full for their losses, backed by major producer countries like Spain, Italy and France.
The BBC's Chris Morris reports from Brussels that Spain in particular has said it expects 100% compensation for its farmers after Spanish cucumbers were initially held responsible for the outbreak.
European farmers' federation Copa-Cogeca quickly rejected the improved EU offer.
"More funds must be made available to help pull the sector out of this deep crisis," said the group's Secretary-General Pekka Pesonen.
Under fire for its handling of the crisis both inside Germany and from the wider EU, Chancellor Angela Merkel's government held an emergency summit in Berlin on Wednesday to assess the situation.
German Health Minister Daniel Bahr was joined by Agriculture Minister Ilse Aigner, EU Health and Consumer Affairs Commissioner John Dalli, government representatives from each of Germany's 16 states, and health experts.
'Get to grips'Mr Dalli avoided publicly criticising the German response, calling instead for European states to co-operate over their response.
"This is not the time for criticism and recriminations, but the time to focus our efforts at all levels in order to get to grips on this crisis," he said.
Continue reading the main story Wash fruit and vegetables before eating themPeel or cook fruit and vegetablesWash hands regularly to prevent person-to-person spread of E. coli strainSource: UK Health Protection Agency
Mr Bahr defended Germany's reaction."The... outbreak in Germany is so severe that we have to react very quickly to announce these recommendations and we still can't give the all-clear," he said.
He also said Germany's health and food safety bodies would undertake an "immediate evaluation" of how they co-operate.
Critics have argued that there are too many different agencies involved in Germany and that this has led to a bungled investigation.
Germany's government is still warning consumers to avoid eating raw foods such as tomatoes, cucumbers, salad and bean sprouts.
The country's national institution responsible for disease control and prevention, the Robert Koch Institute, reported 318 new E.coli-related cases on Wednesday.
"There will be new cases and unfortunately we have to expect more deaths, but the number of new infections is dropping significantly," said Mr Bahr.
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