The Channel Nine crew, who were working alongside a high-profile Australian news correspondent, Liz Hayes, were reportedly confronted in Rinkeby, where the majority of residents are foreign-born.
"Liz Hayes and a 60 Minutes crew are currently on assignment in Europe where they are reporting a story about the migrant crisis," a Nine spokesperson said in a statement widely reported by global media on Tuesday.
"In a suburb of Stockholm yesterday they were confronted by a group who objected to them filming. There was a series of scuffles and the police were called. The 60 Minutes cameraman and producer were slightly injured but filming continued with police at the scene. The crew have now returned to their hotel and are all fine."
Early reports suggested that Australian team had partnered with the Swedish anti-immigration site Avpixlat for the project. However the broadcaster denied this on Wednesday.
Avpixlat describes itself as painting a "non-airbrushed picture" of Sweden, and accuses other Nordic media of suppressing debate on immigration. It has links to the nationalist Sweden Democrats and many current and former politicians from the party write for the site. Mainstream media, including liberal tabloid Expressen and media industry publications Journalisten and Dagens Media, have referred to it as a "hate site" – a description Avpixlat's editor Mats Dagerlind has rejected.
On Tuesday, both Swedes and Australians rushed to social media to question Channel Nine's choice to work alongside the Swedish website.
Foreign news media that come to Sweden and only meet with radical right opinion makers? what is that all about?- Annika Hamrud (@ahamrud) March 1, 2016
Channel Nine did not comment on its decision on Tuesday, despite The Local and other Swedish media seeking the station by phone, email and social media.
However, it later told Australia's Sydney Morning Herald newspaper that it had simply been interviewing Avpixlat staff.
"We categorically deny any suggestion we were in cahoots with this organization, we merely interviewed them in an effort to get all sides of the story," said a spokesman, but admitted that the site had used the 60 Minutes team to push its anti-immigration message.
"I would have thought if you're a right-wing group and you've got Australia's leading current affairs program with you, that you're going to exploit that opportunity no matter how warped your message is."
"They are going to do whatever they can to further their interest," said the spokesman.
Avpixlat said on Tuesday that the foreign TV crew had been keen to film "mass immigration to Sweden" and wanted to add some "local colour" to their report by interviewing residents in Rinkeby.
Liz Hayes (centre) and other Channel Nine broadcasters. Photo: Channel Nine
A spokesperson for Stockholm's police force, Lars Byström, initially confirmed to The Local that police were investigating the attack allegations after being called to the scene on Monday afternoon.
"It happened at around 3.45pm. We were told there was a film team and there were some youngsters who were in the car and there was some kind of argument between the team and then the driver drove over the cameraman's foot."
However he later said that police had decided to close the case, noting that while some media reports suggested that the crew had also been hit or had objects thrown at them by "masked men", no one had come forward in person to make such claims.
"That [the report about the foot] is the only report that I have seen and if someone has been punched please tell them to go to a police station and make a report because we cannot do any investigation based on what is in a paper or on Twitter or Facebook," he told The Local.
He said that in the context of the current available information, "very experienced police officers" had made the decision to focus their resources elsewhere.
The attack allegations quickly grabbed international headlines, including a long article in the UK-based Daily Mail tabloid. The newspaper, which also has a large operation in Sydney, was recently accused by the Swedish Embassy in London of running a sensationalist campaign against the Nordic country's refugee policy.
Sweden took in record numbers of refugees in 2015, but then decided to re-introduce border checks after local authorities said they were struggling to manage the influx.