Alexander and Monica Klein from Malmö were among the first to go through one of the 34 checkpoints that have been set up at Copenhagen airport's Kastrup train station.
“There were no problems. I knew about this so I just had to show my driving licence,” Alexander Klein told the TT newswire.
A total of 150 security staff have been stationed at the airport to oversee the controls. Under the new rules, rail commuters have to exit the train at the airport and go through checkpoints before boarding the train again in order to travel onwards to Sweden. Those without valid ID are refused entry.
It is the first time in half a century that Sweden is demanding photo identification for all travellers from Denmark and deals a blow to Europe's cherished passport-free Schengen system. Only passports, driving licences and Swedish national identity cards will be accepted by the authorities.
The measures are aimed at keeping out undocumented refugees and come after Sweden, which has taken in more asylum seekers per capita than any other European nation, said it could no longer cope with the unregulated flow of new arrivals.
Travellers were warned they could face delays of more than half an hour during rush hour. The journey between Malmö and Copenhagen's main train stations normally takes no more than 40 minutes.
“I won't manage this for very long. I will have to look for another job,” Helena Sjölander, who lives in Malmö but works in Copenhagen, told the regional Sydsvenskan newspaper as she embarked on her journey.
Hedin Argavan, another traveller, told Swedish daily Dagens Nyheter that she had watched the doors to her planned train close after getting delayed by the checks and was forced to wait for the next one on a freezing platform.
"I missed the train because of the identity check. It clearly does not feel fun."
Alexander and Monica Klein who were the first Swedes to have their ID checked when the new control came in. Photo: Johan Nilsson/TT
However by 9.30am Swedish media were reporting that queues at Kastrup were short and moving swiftly.
One commuter, Nicholas Bean, live tweeted his journey, starting with a message that he had arrived by train to Kastrup "where the chaos is supposed to ensue".
But the British expat, who lives in Malmö with his Swedish wife, concluded that there were "no problems" and that the city centre was "if anything quieter than usual".
"I went to Copenhagen from Malmö this morning and apart from trains every 20 minutes instead of every 10 minutes there wasn't much difference. The train ran pretty smoothly," he said.
However he described the process as "ridiculous nonsense", arguing that it was irritating commuters and would likely fail to deter asylum seekers from attempting to reach Sweden.
"It's a sticking plaster on a problem that is much much bigger," he said.
Some travellers who turned up without the right form of identification reported being caught out, as Danish officials refused to accept photo ID cards issued by the Swedish tax office.
Other commentators noted that the checks had been introduced at a time when many Swedes remain off work, ahead of a public holiday on Wednesday. Around 8600 daily commuters are set to be affected by the changes.
"Lots of people are still away," Per Tryding, deputy CEO of the Chamber of Commerce and Industry of Southern Sweden, told The Local from Kastrup, adding that he had been unnerved by the increased security checks.
"It's actually more intimidating than you think when you need to show your identity card like that to a guard and you know they are keeping it somewhere in a cloud."
He argued that the move could deter people from commuting in the region and damage businesses both sides of the border.
"The commuting system is the blood system of a metropolitan economy. It will stop the blood flowing."
Kastrup airport station, where a fence has been put up to stop anyone running across the tracks. Photo: Johan Nilsson/TT
A temporary fence has been erected at the train station to prevent people from trying to slip across the tracks.
“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.
But others have praised the move, suggesting that the controls were necessary.
"I think we need some control (over our borders) but it needs to be very smooth, the commuting back and forth requires balance," Marten Jegenstam, a 41-year-old consultant who lives in Denmark but works in Sweden, told the AFP news agency.
Swedish Migration Minister Morgan Johansson also defended his country's systematic controls, saying they were aimed at "preventing an acute situation where we can no longer welcome asylum seekers properly".
Danish travel operators have said the new measures threaten to cause financial difficulties. The train company DSB has already threatened to levy a supplementary charge on passengers crossing the strait to cover the costs of the checks.
And the Danish HH Ferries Group said it had reported Sweden to the EU for unfair competition after being required to pay for identity checks.
The company argues that the consortium operating the Öresund Bridge, which is partly owned by the Swedish government, was given special treatment because it was not required to help fund the measures.
The Öresund bridge which links Sweden and Denmark. Photo: Johan Nilsson/TT
Several other European Union countries, including Germany, Austria and France, also re-imposed border checks last year as the continent grappled with its biggest refugee crisis since the Second World War.
Almost 163,000 refugees sought asylum in Sweden in 2015, according to the country's migration agency, compared to Denmark's 18,000.