Civil aviation chief Azharuddin Abdul Rahman had been asked to confirm another official's assertion that the two men who boarded missing Malaysia Airlines flight 370 looked "Asian".
The plane vanished early Saturday with 239 people aboard while en route from Malaysia to China.
Azharuddin denied they looked Asian, but he sought to emphasise that skin colour does not indicate nationality by using a reference to Balotelli - a
Ghanaian-born striker with AC Milan and Italian international.
"Do you know a footballer by the name of Bartoli (sic)? He's an Italian. Do you know what he looks like? Balotelli," he told reporters late on Monday.
"I don't want to dwell about this but they (nationality and race) are not the same thing."
Malaysian officials later clarified that there was no suggestion either of the suspect passengers was black, but Twitter users commented that Azharuddin's strained comparison had not helped matters.
One said: "Nice work in looking for the least obvious cause for an airplane crash."
"The case of the missing airplane, somehow, just got weirder," another said.
An extensive sea and land search has turned up no wreckage so far. The plane was flying from Kuala Lumpur to Beijing when it went missing, apparently over waters between Malaysia and Vietnam.
Malaysian authorities, who say they have CCTV footage of the stolen-passport users, have come under increasing pressure from victims' families who have complained of a slow response and inadequate information.
One of the stolen passports was Italian, the other Austrian. The revelation has raised fears of a hijack or terror motive behind the plane's disappearance.
"Yes, I think the Balotelli profile referring to the two phantom passengers is insensitive," another Twitter user posted.
"And you wonder why Balotelli wears 'why always me?'" another one posted, referring to a T-shirt worn once by the controversial footballer after one of his many brushes with authority.