Germany on Monday warned the passport-free Schengen zone was "in danger" after Nordic countries announced new controls at their borders to stem a migrant influx.
"Freedom of movement is an important principle - one of the biggest achievements (in the European Union) in recent years," foreign ministry spokesman Martin Schaefer told reporters.
"Schengen is very important but it is in danger," he added when asked about Denmark's announcement of checks at the German border, on the same day Sweden introduced controls on its frontier with Denmark.
Last week Norway, which is not an EU member but does belong to the Schengen area, said it would start turning back refugees without visas arriving from elsewhere in the Schengen zone, particularly Sweden.
Schaefer said it was "crucial that we in Europe find common solutions" to the worst refugee crisis since World War II, and said the EU must now focus on ensuring the security of its external borders.
Chancellor Angela Merkel's spokesman, Steffen Seibert, said that the Schengen accord, which provides for borderless travel across most of the 28-nation EU, was dependent on better protection of the EU's frontiers.
"We need a common strategy," he said.
Seibert said that Danish Prime Minister Lars Lokke Rasmussen had informed Merkel of his decision before making the announcement.
The migrant crisis, which saw some one million people flooding into Europe in 2015, mostly via Greece and Italy, has sorely tested Europe's commitment to free movement, with several EU members temporarily reimposing border controls as they try to slow the influx.
Seibert noted that Germany, which took in around one million migrants in 2015, had in September also implemented such measures and acknowledged that the Schengen rules allowed such steps in extraordinary circumstances.
Up to 300 asylum seekers leave Germany each day for Denmark, according to Berlin, many of them headed for Sweden, which has received more migrants per capita than any other EU state.
Sweden, Denmark tighten borders
Sweden on Monday imposed controls on travellers arriving from Denmark in a bid to curb an influx of refugees, prompting knock-on measures from Denmark that triggered fresh concern for Europe's Schengen passport-free zone.
Hours after the Swedish controls on a major bridge-and-tunnel link with Denmark went into effect, the Danish government, which fears being saddled with large numbers of migrants, announced it would implement spot checks on its border with Germany.
Alarmed by the restrictions, which come as both Germany and Sweden grapple with record migrant numbers, Berlin warned Europe's Schengen zone was "in danger".
Swedish Migration Minister Morgan Johansson defended his country's systematic controls, saying they were aimed at "preventing an acute situation where we can no longer welcome asylum seekers properly".
The new measures mean that travellers between the neighbouring countries will have to show their ID cards for the first time in over half a century, under a Nordic agreement that predates the 20-year-old Schengen zone.
Danish Prime Minister Lars Lokke Rasmussen cited the Swedish checks to justify his own country's immediate introduction of random border controls.
"We are simply reacting to a decision made in Sweden ... This is not a happy moment at all," he told reporters.
Rasmussen warned Sweden's controls could have a domino effect on Denmark, which received just 21,000 asylum requests in 2015, compared to Sweden's 163,000.
He said 91,000 migrants and refugees had crossed the border from Germany into Denmark since September, of whom 13,000 had sought asylum in Denmark.
"It's clear the EU is not able to protect its outer borders and other countries are going to be forced to introduce ... border controls," he said, adding: "Europe's leaders must react to this."
Under Schengen rules, countries are allowed to re-introduce temporary border checks in exceptional circumstances.
Extra security staff were on hand Monday at the Danish side of the Oresund crossing, a major entry point for migrants and refugees hoping to start a new life in Sweden.
The controls proceeded smoothly but travellers were warned to expect longer queues and delays during the early evening rush hour when commuters with jobs in Denmark return home to Sweden.
Tens of thousands of journeys are recorded on the bridge each day, including 8,600 people who commute between jobs and their homes in Copenhagen and the southern Swedish city of Malmo.
Under the new rules, all rail passengers now have to exit the train at Copenhagen airport's Kastrup station and clear checkpoints before boarding again.
A private security company at the station could be seen checking and photographing traveller IDs before allowing passengers on trains.
'A Berlin Wall'
Officials at Danish train operator DSB confirmed a small number of people had been turned away, but would not specify if they were migrants or just commuters lacking proper ID.
"If they don't have photo ID then we say sorry, we can't let you on board," DSB spokesman Tony Bispeskov said.
Temporary fencing has also been erected at Kastrup station to prevent people from trying to sneak onto Sweden-bound trains.
"It's as if we are building a Berlin Wall here. We are going several steps back in time," said Michael Randropp, a spokesman for the local Kystbanen commuters' association.
The new measures come after Sweden -- which has taken in more asylum seekers per capita than any other EU nation -- said it could no longer cope with the unregulated flow of new arrivals.
Several other EU countries, including Germany, Austria and France, also re-imposed border checks last year as the continent grappled with its biggest refugee crisis since World War II.
More than one million migrants reached Europe in 2015, most of whom were refugees fleeing war and violence in Syria, Afghanistan and Iraq, according to the United Nations refugee agency.
Joakim Ruist, a macroeconomist and migration researcher at the University of Gothenburg's School of Business, said Europe would eventually have to forge a new refugee policy.
"In the end they're going to reach a point where it will be so costly and painful, that it will actually be less painful to sit down and try to hammer out a new refugee policy," Ruist told Swedish news agency TT.