Denmark said it was starting the immediate introduction of controls at the German border, with Danish Prime Minister Lars Lokke Rasmussen holding a press conference on Monday to explain his decision.
The announcement was made just hours after Sweden introduced controls on its frontier with Denmark to stem a migrant influx.
"When other Nordic countries seal their borders it can have major consequences for Denmark," Rasmussen said, referring to the Swedish measure.
"It can lead to more asylum seekers," he told reporters in Copenhagen, before suggesting that other EU member states would likely follow suit.
"It's pretty obvious that if the European Union can't protect its external borders, you will see more and more countries forced into introducing internal border controls," Rasmussen said, describing Denmark's decision as "not a happy moment".
The new controls took effect at midday and will initially last for 10 days. After that time, the border controls can be extended by 20 days at a time as the situation warrants, the PM said.
"This is a major step and it should be seen in light of the serious migration and refugee crisis that Europe is facing. [It is] likely the biggest and most complicated crisis we have seen this century," Rasmussen said.
The border controls at the German border will not be a "one to one" copy of Sweden's model in which private transport companies are tasked with checking the identification of all passengers. Instead, Danish police will carry out random checks on ferries and trains arriving from Germany.
"Not everyone from Germany will be checked. The police will not ask everyone to show their passports," Rasmussen said.
He added that Denmark wants to avoid the "chaos" and "serious disruptions" some have predicted will be created by Sweden's border controls, which are expected to cause significant delays for the roughly 8,600 daily commuters between Copenhagen and the southern Swedish city of Malmö.
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The PM said he informed German Chancellor Angela Merkel of his decision earlier on Monday.
Germany on Monday said it saw the passport-free Schengen zone "in danger" after Sweden and Denmark 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.
The refugee crisis has been a major point of contention between Sweden and Denmark. Sweden took in over 160,000 asylum seekers in 2015, the highest proportion per capita in the European Union, while Denmark has received just 18,000.