Okon, who finished sixth in the 110m hurdles final, tested positive for the banned stimulant methylhexanamine, said Mike Fennell, the Commonwealth Games Federation president.
On Monday, it was revealed that Nigeria's women's 100m gold medal winner Osayemi Oludamola had also tested positive for the same substance.
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"On anti-doping, we have now conducted 1,200 tests and again I regret to inform you that a second athlete has tested positive," said Fennell.
"It is Nigerian 110m hurdler Samuel Okon who tested positive for the same substance (as Oludamola)."
He said a provisional hearing would be held into the matter later Tuesday but that Okon had waived his right to have a B test.
Fennell added that his team had held talks with the Nigerian delegation about the embarrassing test results and he was "satisfied they are taking the matter very seriously."
