Denmark's eastern island of Zealand, where Copenhagen sits, was cut off for hours as soldiers and police launched a massive manhunt.
The Oresund Bridge, which connects Denmark with Sweden, was closed in both directions at around 1pm UK time.
The Great Baelt Bridge between the Danish islands of Sjaelland and Fyn was also closed and ferry crossings to Germany and Sweden were cancelled.
At about 3.20pm UK time, police said all bridges and ferry crossings were being re-opened, sending thousands of travellers on their way again.
A police helicopter and dog squads were spotted on a highway near Roskilde, 40 miles west of the capital Copenhagen, according to Denmark's TV2.
Police had issued an appeal for sightings of a black Swedish-registered Volvo car, saying there were likely to be three people inside involved in "serious crime".
Later they said the car had been found but there was no word on the people inside or any arrests.
Copenhagen police spokesman Joergen Bergen Skov said: "We have found a vehicle that we believe is the right one.
"There is no reason to be worried."
Sweden's Aftonbladet newspaper had earlier quoted an unnamed police source as saying the car was being sought in connection with a kidnapping.
Hans Jorgen Bonnichsen, the former head of operations at the Danish Security and Intelligence Service (PET), told local media: "I spent 41 years in the Danish police, I have never seen such a big action taken before."
Denmark's armed forces said they had taken part in the operation but gave no further detail.
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