His departure was announced during a routine meeting of the Federation’s General Assembly.
According to the Libya Observer, a bilingual online publication based in Tripoli, Al-Shalmani made his resignation public on Sunday.
He expressed his sentiments by stating, “I do not wish to be associated with the shortcomings in Libyan sports.”
“We faced difficulties during the previous period.
“I thank all members of the General Assembly, and I forgive everyone from all segments of the sports sector.
“I have a history in the International, Arab and African Federation, and no one can deny that.”
Tensions are escalating between Nigeria's Super Eagles and the Libyan national team as they prepare for Tuesday's All African Cup of Nations qualifier.
Upon their arrival in Libya, the Super Eagles reportedly faced 'inhumane treatment' from local authorities.
They were left stranded at Al Abraq International Airport for more than 15 hours, which appeared to be an act of retaliation.
However, Ademola Olajire, the director of communications for the Nigerian Football Federation, confirmed that the team was en route back to Nigeria.
In response to the situation, the Libyan Football Federation stated that the delays experienced by the Nigerian team were due to standard air traffic and logistical issues, rather than any intentional misconduct.