Research firm Strategy Analytics said on Friday that Samsung's operating profit for its handset division stood at $5.2 billion in the second quarter, topping Apple's estimated iPhone profit of $4.6 billion. This marked the first time the Korean firm has overtaken its U.S. rival.
"Apple's profit margin for its handset division has been fading recently due to lacklustre iPhone 5 volumes and tougher competition from rivals," Neil Mawston, the executive director at Strategy Analytics, said in the research.
But a critic at Apple fan website Apple Insider claimed that Friday's report was inaccurate.
"Strategy Analytics' creative accounting, designed to award Samsung with an contrived achievement, appears to be a distraction from reality, rather than real information," said Daniel Eran Dilger, a writer at Apple Insider, which gives news and tips on Apple products and company information.
Dilger said Strategy Analytics had estimated Apple's iPhone profit in a simplistic manner, by halving its total reported profit of $9.2 billion. In addition, he complained that Apple's iPhone profit had been directly compared with Samsung's profit from its IT and mobile communications division, even though the unit also includes tablets and personal computers.
Strategy Analytics maintained that it compared Apple's handset profit directly with Samsung's, and excluded other devices such as PCs. Nonetheless, the Apple Insider article created a buzz on Twitter, with many Apple fans re-tweeting the story. The debate comes at a time of fears the smartphone market is becoming saturated, and that weaker growth in China could harm the sector's outlook.
Apple Insider said that Apple and Samsung Electronics were likely to be making similar profits. But Benedict Evans of consultancy firm Enders Analysis told CNBC that it was hard to calculate exact numbers for Apple's operations.
"Apple doesn't have an iPhone division as such, and the operating costs are largely common across iPhone and iPad. So calculating an iPhone operating profit is pretty tough," he said.
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Strategy Analytics has tracked Apple and Samsung's profits for handsets for the past 7 years. It used similar methodology to report that Apple's mobile phone profit had overtaken Nokia's in the third quarter of 2009, a finding that Apple Insider cited on its website at the time.
—By CNBC's Matt Clinch