His resignation comes barely four months after Mr. Owusu was accused of financial misappropriation at the company.
He is alleged to have superintended over questionable expenditure at the authority, including spending a million cedis to renovate his official residence.
Government subsequently instituted a probe into the matter.
But Transport Minister, Kwaku Ofori Asiamah revealed the report of the probe is yet to be completed. He told journalists at the meet the press encounter Tuesday that Mr. Owusu resigned having attained the age of 65.
Controversial musician cum politician, Kwame A-Plus, in October 2018, posted on Facebook, documents requesting approval for payment of GHȼ135,125 in one night, on food, drinks and music, for an end-of-year dinner party on December 22, 2017.
The amount, according to A-Plus, was paid to Luxe Suites Hotel where CEO of the GMA, Mr. Kwame Owusu, also holds the position of Group Chairman raising concerns of a possible conflict of interest.
On a separate occasion, a request was made by the Director, Administration, for the payment of GHȼ10,652 to the same Luxe Suites Hotel for food and drinks for eight people at a meeting.
The Transport Minister subsequently instituted investigations into the incident.