Mr Junker said justice and fundamental values have taken priority in all accession talks of new countries to the European Union and Turkey has not shown it shared these.
The President said: “For some considerable time, Turkey has been moving away from the European Union in leaps and bounds.
“Journalists belong in editorial offices amid heated debate and not in prison.
“I appeal today to the powers that be in Turkey: Let our journalists go.
Stop calling our member states and members of governments fascists and Nazis.
“Europe is a continent of mature democracy, those who knowingly offend pull up the drawbridge and sometimes I have the impression that there are those in Turkey who want to pull up the drawbridge and later blame the European Union for the failure of accession negotiations.
“From our side, there will always be an outstretched hand, outstretched to the great people of Turkey and all those who are willing to work with us on the basis of our shared values
The majority of German have said they oppose Turkish EU membership and say accession talks with the country should end.
Halting accession talks with Turkey would be a strategic mistake by the European Union, Greek Prime Minister Alexis Tsipras has said.
The EU chief set out his year plan to ensure the bloc can deal with the migration crisis and reforming the eurozone.
The Brussels boss has also called for EU integration in the face of rising populism after Britain voted to sever ties with the bloc ahead of crunch elections in Italy, Sweden, Hungary and the Czech Republic, where eurosceptic parties are gaining momentum.