Siasia had earlier requested for a return to Lagos with hopes that it will spark up life into the team.
However, events in their friendly game against Sierra Leone on Wednesday proved otherwise as the team was booed by Lagos fans towards the end of the game that finished 2-1.
Siasia also complained about the synthetic pitch of the Teslim Balogun Stadium saying it affected the play of his lads.
The game on March 27 was originally scheduled to hold in Lagos, with Wednesday's friendly against Sierra Leone seen as a dress rehearsal for the qualifier, but a series of hiccups and players' complaints about the artificial turf has forced a change in thinking.
"The game will be played in Kaduna," NFF Executive Committee member Christopher Green told KickOffNigeria.com on Thursday.
"The executive committee will meet to ratify the decision but Lagos is definitely out."
It will be the first time the Super Eagles return up north, after the unhappy memories of playing Angola in a 2006 World Cup qualifier in Kano which they drew 1-1 and eventually meant they did not qualifier to play in Germany.