A member of Gabon's football federation (Fegafoot) was arrested on the tarmac of Libreville's international airport moments after the team's plane returned from the Africa Cup of Nations on Tuesday.
The arrest is part of the Gabonese government's inquiry into alleged widespread sexual abuse in football following allegations reported by a British newspaper.
Mombo has denied any wrongdoing.
Five members of Gabon's football community have now been arrested following allegations made against of them of raping and sexually abusing minors.
These include Patrick Eyi, a former coach of Gabon's national Under-17 team widely known as 'Capello', as well as three local lower-tier coaches.
Mombo 'was a predator'
Prior to December's arrest of Capello - who denies allegations he raped and sexually abused young footballers - Gabon's Sports Ministry had said the sexual abuse of minors in the country by multiple accused perpetrators could number 'hundreds of alleged victims'.
BBC Sport Africa has sought comment on the case from Gabon's Sports Minister but received no reply.
Gabon's President Ali Bongo, meanwhile, has previously described the claims as "very serious".
Mombo is accused of sexually abusing young players and demanding sex as a condition of them securing places in national teams.
"Serge Mombo was a predator," one alleged victim told the Guardian earlier this month.
Mombo has blamed the allegations on his re-election as head of Gabon's senior football league last June and questioned the timing of the piece, as it came out on the eve of Fegafoot's executive committee elections.
"I was an international referee, am today president of the league and I have never been in the centre of these things which I condemn," he said earlier this month.
"I am going to use all legal means to clean my reputation."
Fifa investigation opened
Following the reports, investigations have been opened by football's world governing body Fifa, the Gabonese government as well as Fegafoot.
"Given the seriousness of the allegations being made, we can confirm that Fifa's independent ethics committee has opened an investigation and is currently looking into the matter," said a Fifa spokesman.
While in Cameroon, Fegafoot's media officer explained that his organisation has launched an internal investigation to "effectively encourage the victims to speak out [and] allow young people to free themselves."
"The Gabon football federation is co-operating with Fifa's independent ethics committee to get to the truth," Moussa Ngoma told BBC Sport Africa.
"We want to get to the truth. The ethics commission has put measures in place to permit those involved with football to denounce this kind of thing."
"We are talking about paedophilia - the taking of innocence - it is completely reprehensible. The people who carry out these crimes will be punished. It is important to let justice do its job and that's the position of the football federation."
Support for alleged victims
One of Gabon's squad members at the Nations Cup, winger David Sambissa, expressed his support for the alleged victims and hopes that the various investigations by the government, Fifa and Fegafoot can determine the truth.
"I am sad about the people involved - the victims - they have all my support," he told BBC Sport Africa.
"I leave this to the politicians, police and people in charge to take care of it."
One alleged victim told The Guardian that sexual abuse of minors in Gabonese football has been the 'reality for decades'.
However, it is not just football that has been affected by paedophilia claims - with two tennis officials and another from taekwondo having been arrested in recent weeks following accusations made against them.
In court earlier this month, taekwondo official Martin 'Chaka' Aveira admitted having abused minors in the sport.