Partey had been accused of reporting for duty just two days before the squad were scheduled to fly to Rabat for the game against Morocco.
But Ghana have now clarified Partey's absence in a statement.
They said: "Thomas travelled to Cape Coast on Thursday to meet Coach Charles Akonnor over some personal issues.
"After the meeting which lasted for about an hour, the Coach excused him from the trip to Morocco – and asked him to report to camp for the second game against Ivory Coast.
"As the deputy Captain of the Black Stars, Thomas later joined his colleagues in training to show solidarity and support before leaving for Accra. The Arsenal midfielder will therefore team up with the rest of the squad on Thursday when the team returns from Morocco."
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