Fishing ministers from across the bloc are coming together this week to set fishing quotas in the North Sea and Atlantic for 2018.
But the EU Commission has infuriated the German authorities with demands for a total ban on eel fishing.
Eels are facing extinction due to massive overfishing – but Germany does not believe a fishing ban is the answer.
German agriculture minister Christian Schmidt said: “A complete ban on eel fishing is not considered appropriate.”
He said it was right that eels should be protected, however, but said a complete ban was not necessary.
Mr Schmidt said: “That can not lead to the fact that in Germany catching eel in inland waters is completely stopped.”
German fisherman have taken part in management programmes designed to protect eels, helping the population to recover in the face of overfishing.
Mr Schmidt pointed out Germany had played its part in this as he vehemently opposed the fishing ban.
It comes as British fishermen also hit out at the EU over punitive fishing quotas, with the issue becoming a driving force behind last year’s Leave victory.
They demanded urgent changes to the quotas after having to throw back fish worth £10,000, which may have died after being returned to the sea.
British fishermen want a change in the regulations as they are being forced to throw away thousands of tonnes of high quality sea bass.
Skippers say growing numbers of the fish are being accidentally caught as part of their haul of mackerel, herring and other species.
But EU rules designed to protect sea bass from over-fishing state catches with more than three per cent sea bass must be thrown back.
A delegation of fishing bosses are joining Defra minister George Eustice in the European Union this week in an attempt to resolve the long-standing issues.
While Paul Treblicock, chief executive of the Cornish Fish Producers Organisation, said new rules had to be worked out despite Brexit.
He said: “For the next year at least the UK is a fully fledged member of the European Union so we have to put Brexit aside and negotiate the best possible deal for the UK fishermen for 2018.
“French fishermen don’t want to throw away perfectly good sea bass any more than we do. They agree with us that something has to change.”
A decision on fishing quotas is expected to be taken by all 28 EU fisheries ministers this Wednesday.
Additional reporting by Monika Pallenberg