The defence headquarters has denied cancelling training programmes for female combatants.
It said a news report claiming the programmes had been scrapped was "an act of disinformation."
The military said all female officers would continue to enjoy the same career benefits available to their male counterparts.
The Punch Newspaper reported the story on Monday, saying the Nigerian Army, Navy and the Air Force cancelled the inclusive programme at the Nigerian Defence Academy after complaints by unnamed Muslim leaders.
"The northern Muslim leaders want to prevent a situation where one day, a woman will lead the army and give orders to men," the paper reported citing an anonymous military personnel.
The report also suggested that the northern elements were opposed to the programme because it was particularly popular amongst southern females who are predominantly Christian.
But John Enenche, a major general and spokesperson for the Defence Headquarters, said the story was false.
"The contents of all those publications are ill-intended concoctions, not authentic and should therefore be disregarded completely," Mr. Enenche said.
The extant "provision in the terms and conditions of service for female officers of the Nigerian military is that 'They are eligible for all the types of commission that are grantable to their male counterparts', which has not changed," Mr. Enenche said.
Punch did not immediately respond to PREMIUM TIMES requests seeking comments Tuesday evening.
Mr. Enenche did not immediately respond to PREMIUM TIMES requests seeking further details.
Former President Goodluck Jonathan implemented the changes to incorporate female officers into regular combatants roles, after decades of discriminatory practices that had made it difficult for women to aspire to the top leadership positions in the military.
The policy, which was adopted in 2010 with first female intakes starting in 2011, made it possible for a woman to become the Chief of Army Staff or its equivalent in the Navy and the Air Force. About four dozen women were said to have enrolled as regular combatants since the policy commenced.
The report that it had been cancelled with the awareness of Mr. Buhari sparked outrage on Monday as citizens feared it was a triumph of misogyny that could drag the country's social development backwards, prompting the Defence Headquarters to push back with its position Tuesday evening.