The youngster was the subject of transfer speculations last week, with reports claiming the starlet had signed a deal worth £2 million at Etihad Stadium.
He caught the eye of scouts at a youth tournament in Qatar.
''WAFASC will like to debunk circling reports and publications in the media that our player Aminu Mohammed has been transferred to a foreign club," the Ghanaian club said in a social media statement.
''We wish to categorically state that Aminu Mohammed is still a player of WAFA SC.''
Aminu is currently in Ghana's camp ahead of the upcoming Under-17 Fifa World Cup in India next month.
The 16-year-old, who missed the U-17 Africa Cup of Nations in May due to club commitment, had a training spell with Austrian side Red Bull Salzburg, after which he joined City on a trial.