Denmark is to re-instate permanent customs checkpoints at its borders and introduce video surveillance of cars entering the country.
Politicians from the centre-right government say it the change is aimed at stopping crime and illegal immigration.
But Germany and the EU said border checkpoints violate rules on unrestricted travel in the Schengen zone and regulations on free movement within the bloc.
Responding to European Commission President Jose Manuel Barroso saying the measures could contravene European Union rules Denmark insisted it is not breaching its international obligations.
“This is a matter of reinforced customs control where we will go after illegal import of, among other things, narcotics, weapons and large amounts of money, precisely as we do today,” Tax and Customs Administration director Erling Andersen said.
An opposition motion to scrap the plan was voted down in the chamber on Friday and parliament’s finance committee then approved the government’s request for funds to pay for the measures, officials said.
Customs controls at frontier crossings and on international trains will be increased gradually and the new measures are to be fully implemented by early 2014.