Ghana, who reached the quarter-finals of the 2010 World Cup in South Africa, are now relying on results going their way if they are to book their ticket to Russian Federation.
The Uganda Cranes will tomorrow take on the Black stars of Ghana in the 2018 FIFA World Cup Qualifiers Group E game at Namboole stadium.
At the last minute of the match between Ghana and Uganda on Saturday, a referee disallowed the goal scored by Black Star player Raphael Dwamena.
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Kwesi Appiah's side now has a long list of absentees, including captain Asamoah Gyan and deputy captain Andre Ayew, as well as Agyemang Badu, John Boye, Harrison Afful Jordan Ayew and Thomas Agyepong and Christian Atsu.
"We failed to beat Ghana on Saturday because the pitch was not to our advantage as hosts", Onyango told KweséESPN.
Ghana will play the Pharaohs of Egypt in their final round of the qualifiers in November.
If Ghana had won against Uganda, they would now be in second place in Group E, with eight points to Egypt's nine.More news: Auto mounts pavement outside London museum, according to reports
Ghana had been denied a penalty earlier in the half while several other decisions raised questions about the officials, it added.
"These and several other decisions by the match officials have left the GFA with no option than to ask Federation Internationale de Football Association to examine their performances".
By Saturday's match result, the Black Stars are all but out of the race to Russian Federation 2018 as Egypt will secure the sole Group E ticket should the Pharaohs account for bottom-placed Congo on Sunday.More news: Ireland stick with Martin O'Neill and Roy Keane