Presidential spokesman Mahama Ayariga said in a statement that the inquiry should be carried out to ascertain the cause of deaths and find preventive measures to avoid a recurrence.
Doctors at the Okomfo Anokye Hospital in Kumasi said at least four fans died out of severe suffocation after they had been rushed there from the stadium.
The poster fixture of the Ghanaian domestic season drew a full house, with many fans getting in as early as 09h00. By kick-off time at 14h00, the stadium was overflowing with fans, with aisles in between seats and exits completely taken over by fans.
President Mills said he acknowledges the effort of the security agencies and other well-meaning members of the public to ameliorate the situation, but believes an inquiry is needed.
Many observers believe the ticketing arrangement and security for a game that has traditionally attracted the biggest crowds in Ghana football was flawed.
And KickOffGhana.com saw videos of fans scaling the stadium walls to gain access into the grounds while in some cases, security men detailed the control of access took monies and helped some fans scale the wall.
All that is bound to come under scrutiny when the presidential probe takes effect.