The probe comes after the secretary general of football's world body Fifa, Fatma Samoura, instructed Fecafoot president Seidou Mbombo Njoya via an email dated 18 February - seen by the BBC - to look into the matter.
"We have been informed by the secretary general of Fifpro [global players' union] Theo Van Seggelen and the president of Cameroon's player union Geremi Njitap of the non-payment of salaries and bonuses to players from 24 clubs in Cameroon's top and second tier championship," wrote Samoura.
"It is Fecafoot's responsibility to ensure that players' rights are respected, and the non-payment of salaries and bonuses - with some dating as far back as the 2017-2018 season - is unacceptable.
"We are asking you to take urgent measures to bring an end to this situation and ensure that the footballers from these 24 clubs receive their wages," Samoura added.
Fecafoot officials have been given a deadline of 4 March 2019 to rectify the situation.
Earlier this month, former Cameroon international Geremi Njitap, who now heads the country's player's union Synafoc, stated that 24 of the 33 professional clubs in the country had failed to meet their monetary obligations.
The former Real Madrid and Chelsea defender disclosed that a majority of players in the top two leagues lived in difficult conditions with teams failing to pay salaries and bonuses for months.
"It is very disheartening to know that some of these players give their best on the pitch and yet wallow in abject poverty because some club presidents chose to do the wrong thing," Geremi told BBC Sport.
"Some of these players don't even have contracts, and even when contracts exist, the terms aren't respected. There are those who've been with teams for two seasons and haven't had any wages. This must come to an end.
"We are very glad about Fifa's reaction and we're hopeful this will bring an end to this problem. Some of them can't pay their rent, they live in terrible conditions and find it daunting caring for their families. Players deserve better," Geremi said.
Since Fifa's intervention, Cameroon's professional football league has paid out a grant of 84 million FCFA, approximately US$145,252 to the clubs, with each top league outfit taking home three million FCFA with second tier teams receiving 2 million FCFA.
Last season, only six out of the 18 top flight teams, and three of the 15 second division sides honoured their financial obligations with the players.
At the time of writing, defending champions Coton Sport of Garoua, alongside 2018 Cup of Cameroon winners Eding Sport, Yong Sports Academy, Bamboutous of Mbouda, Stade Renard and UMS loum are the only top flight teams to have met their agreement with the players.