Omagbemi's contract expired at the end of their triumphant 2016 Women's Africa Cup of Nations campaign in Cameroon.
Despite being one of the 10 names on Fifa's list for Women's Coach of the year, Omagbemi's name does not appear on a shortlist published by the Nigeria Football Federation (NFF) for various positions in the national teams.
"I'm shocked and surprised that I was not even considered again or shortlisted for the role," Omagbemi told BBC Sport from her base in the United States.
"I actually reapplied for the job even though I felt I had done enough to continue as coach of the Super Falcons.
"I feel honoured to have served my country as coach and I thank the NFF for that great opportunity, I have absolutely nothing against the federation or anyone there.
"I must also thank the players, my backroom staff and everyone in Nigeria for the support, which helped us immensely to achieve the targets given to us," Omagbemi added.
BBC Sport understands that top NFF officials were left upset by Omagbemi's failure to submit her tournament report at the end of the biennial African Women's Nations Cup in Cameroon last year, as clearly stipulated in her contract.
The NFF's hierarchy also questioned Omagbemi's managerial conduct during the Super Falcon's protest over unpaid win bonuses.
But Omagbemi has refused to be drawn into a war of words with her former employers over her controversial exit.
"If that's the path they want to follow, I can only wish them all the best and the country more success," Omagbemi said.
The former international, who played in four Fifa Women's World Cups, went several months without pay during 2016.
Despite suffering the death of her father prior to the tournament in Cameroon, Omagbemi became the first woman to win the competition as both player and coach.
She then made her swift journey to Warri, southern Nigeria, for the burial of her father, away from the bonus protest by her team which marred the country's triumph.
Six months after her success at the Women's Africa Cup of Nations, she also lost her teenage son in tragic circumstances in Warri.
"I've had to deal with a lot since the end of that tournament in Cameroon, but that's life," said Omagbemi.
Omagbemi was hoping to follow in the footsteps of her predecessors Eucharia Uche and Edwin Okon, who both won the Women's African title and then led the team to the 2011 and 2015 Women's World Cup respectively.
Nigeria have dominated women's football in Africa having been crowned champions a total of eight times with Equatorial Guinea the only other nation to have won the continental title.
The qualifying round for the 2018 Women's Africa Cup of Nations in Ghana has been scheduled for February 2018.
Nigeria are the only African team to have played in all Fifa Women's World Cup tournaments since 1991.
But they have failed to translate their continental dominance on the world stage, as their best performance came in the USA in 1999 when they reached the quarter-finals.