The national team coach is facing questions over his decision to attend Tuesday's media roundtable instead of participating in the technical committee's proceedings in Abuja
The Super Eagles trainer had instead chosen to attend a reception and media roundtable organised by national team sponsors TomTom in Lagos.
The NFF has issued a query to the trainer in which it has also asked him to respond to other issues including missing the reception by the president in February and travelling without informing the federation.
"It is important we draw your attention to previous actions whereby you travel out of Nigeria without NFF's express permission," the NFF wrote to Keshi in a letter widely circulated in the media.
"Specifically, you travelled out of Nigeria before 13 February 2014, the day President Jonathan received the Africa Nations Championship (CHAN) team, causing us huge embarrassment.
"Your request for leave approved by the NFF was from 15 February - 10 March 2014 but you left before 13 February and returned 26 March.
"The Technical Committee meeting on 25 March was called off because you said you had flight hitches from USA.
"As a responsible organisation, we have no other option than to issue you a query to explain how all these events unfolded," wrote Emmanuel Ikpeme, the NFF's director of technical.
He is expected to respond within 24 hours.
On Tuesday, Keshi told media that he was not at loggerheads with his employers and assured that they both enjoyed cordial relations.
"My relationship with my bosses is good, I don't have a problem with them," he said.
This new development is certain to strain the relationship between the former national team captain and the federation as Nigeria prepare for the World Cup in less than four months.