"The story was a draft that shouldn't have been published," Niels Pinborg, editor-in-chief of Se og Hør told The Local after an article headlined "King Carl Gustaf suspected of murder" appeared on the publication's website.
The news item, which appeared on Friday, has since been removed.
A spokesperson for the Swedish Royal Court called the article "unlawful", telling Danish media magazine Journalisten removing the story was "wise".
"Errors happen all the time. We proved we are able to undo wrong decisions," Pinborg told The Local.
The Danish paper's unsubstantiated accusation against King Carl XVI Gustaf appeared following the killing of reputed Swedish underworld figure Mille Markovic, who was gunned down in his car last week outside central Stockholm.
The original article said the Swedish king had a potential motive to kill Markovic, after the former released images of the regent at Privé, a sex club once owned by the convicted criminal. However, experts later proclaimed the images had been faked.
"It could be a contract killing," the article read. "And the king is among the persons who has a motive to get rid of the Serbian-born Mille Markovic."
The editor-in-chief regretted the article had been published with such pointed claims, admitting to Journalisten that "the headline in particular was almost libelous".
However, he added that he still believes the story about the king's rumoured involvement in the killing to be a "spectacular" story, saying that Se og Hør is considering publishing a different version of the story.
Speaking with The Local on Tuesday, however, Pinborg refused further comment.
"I have no further comment, because any repetition of the wrongful claims in the story would be damaging to the Swedish king," he said.