Sweden began checking documents of travellers from Denmark on Monday for the first time in half a century, causing delays of up to 50 minutes for trains and buses crossing the 4.9 mile (7.9 km) Oresund Bridge, Europe's longest combined road and rail bridge. However private vehicles were exempt from the checks.
Denmark's prime minister said Sweden's move gave his country no option but to impose its own border controls and he appealed to the European Union to take "collective decisions" to better protect its external borders against the tide of migrants.
"The Swedish ID checks can increase the risk of a large number of illegal immigrants to accumulate in and around Copenhagen," Lars Lokke Rasmussen told a news conference in Copenhagen, justifying the new controls on the German border.
Last year some 163,000 refugees sought asylum in Sweden, the largest number for any EU country relative to its population. But with arrivals running at around 10,000 a week in November, mostly travelling through Denmark, the Swedish government has said it is time to tighten border controls and asylum rules.
"A dark day for our Nordic region," former centre- right Swedish foreign minister Carl Bildt said on his Twitter feed on Monday to describe the imposition of border checks.
Thousands of commuters daily use the Oresund Bridge - familiar to fans of the 'Nordic noir' crime drama series "The Bridge" - to shuttle by car, train and bus between the Danish capital Copenhagen and the Swedish city of Malmo.
Travellers expressed dismay at the new checks.
"I paid 230 euros for these tickets. This is Europe, not Africa. Why these checks?" said Gezahegn Abebe, an Ethiopian migrant living in Norway as he stood in the train station by Copenhagen airport before trying to head to Sweden.
Returning home from a visit to Germany, Abebe said he had not been allowed through by security guards when he showed his Norwegian residence permit. Unlike Sweden and Denmark, Norway is not in the EU but it is a member of the Schengen zone.
"They said this is not a passport. If you don't have a passport you can't go," Abebe said.
More than one million migrants fleeing conflicts and poverty in the Middle East and beyond sought shelter in Europe in 2015 and many more are expected to come during 2016.
The unprecedented numbers have strained to breaking point the EU's free movement policy and its attempts to create a single economic area, with several countries temporarily re-introducing border controls.
Rasmussen said the Danish border controls would last for 10 days but could be extended.
Officials in Germany, which itself is struggling to absorb about a million migrants who arrived during 2015, said they were paying close attention to the new Danish border checks and their possible impact on the northward flow of migrants into Denmark.
Sweden has long been proud of its self-proclaimed status as a 'humanitarian superpower' and its decision in November to tighten border controls and asylum rules came close to bringing down Prime Minister Stefan Lofven's minority coalition government of Social Democrats and Greens.
Norway swiftly followed Sweden's lead and has announced 40 proposals to tighten asylum rules.
ID-free travel within the Nordic region - long a popular magnet for migrants due to its high standards of living and generous social welfare benefits - dates back long before the Schengen accord to the 1950s, when Norway, Sweden, Denmark, Finland and Iceland signed a passport union.
Around 15,000 commuters cross the strait between Sweden and Denmark every day and there are worries that businesses in Sweden's Skane region and in Copenhagen will be hit.
Denmark's state-owned rail operator said the ID controls would cost it nearly 1 million Danish crowns ($147,000) a day.
Danish employers fear fewer Swedes will want to cross the bridge to work in Denmark as a result of the new rules.
"Already now the lack of workers is a problem and if the Swedes do not want to work here due to a longer commute, the problem will be even bigger," Pernille Knudsen, Vice Chief Executive of the Confederation of Danish Employers, told Danish newspaper Borsen.
"The Swedish border control is a potential killer of growth for the Danish economy."