The federation boss remains confident that Harambee Stars will still make it to 2014 World Cup final despite Nigeria getting a late goal to deny Adel Amrouche's boys
The Stars led for most of the match after Francis Kahata had scored from the free-kick in the 36th minute but a late goal by Oduamadi Nnamdi ensured the Africa champions got at least a point from the match.
Nyamweya complained about poor officiating in Saturday's fixture and took issue with the added time.
"There was nothing to warrant additional five minutes in the game. We were clearly robbed of victory," he told Goal.com.
He added, "For the African champions to struggle to get an equalizer it clearly shows that our game is improving. Kenyans must keep supporting this team. The future looks bright."
Nyamweya pleaded with local fans not to give up after the result insisting there is still a chance for the team to do better in future matches.
After Saturday's result, Kenya are last in their Group with two points. Malawi lead in the Group with five points after they upset Namibia away.