Prince Ali of Jordan said he has asked soccer's governing body to investigate the new Memorandum of Understanding signed in Kigali, Rwanda, on Friday.
Ali claims the agreement will allow the two confederations, which have 100 of the 209 member nations between them, to bloc vote on February 26.
He believes it will give rival candidate Sheikh Salman bin Ebrahim al-Khalifa -- head of the Asian Football Confederation -- an unfair advantage.
"I am concerned that there has been an attempt to breach electoral rules in the FIFA presidential election," Ali said in a statement Saturday.
"I have written to the FIFA Ad Hoc Electoral Committee informing them of my concerns and asking them to examine the matter.
"I have always promoted cross-regional understanding, however the timing of this MOU between the AFC and the CAF looks like a blatant attempt to engineer a bloc vote."
Ali was defeated at last year's FIFA elections by incumbent Sepp Blatter, who subsequently stood down in the wake of a U.S. corruption investigation targeting many of the body's top officials.
Blatter, who took the top job in 1997, has since been banned for eight years along with UEFA president Michel Platini for a 2 million Swiss Francs ($2 million) "disloyal payment" between the duo that FIFA's ethics committee ruled was a breach of its regulations.
Both have stated their intent to appeal, while FIFA is seeking a longer suspension.
Platini had been expected to succeed Blatter, but has withdrawn his candidacy.
Five men will stand next month, including UEFA general secretary Gianni Infantino, former FIFA official Jerome Champagne and South Africa's Tokyo Sexwale.
Africa is the largest of the confederations with 54 members, while Europe has 53, Asia 46, North and Central America 35, Oceania 11 and South America 10.
Ali claims that the Asian-African agreement continues the corrupt activities that has brought FIFA into "disrepute" in recent years.
"Africa's proud football associations are not for sale and development resources belonging to national football associations should not be used by presidential candidates and confederation presidents for political expediency," he said.
"Questions must be asked: Was this deal approved by the members of the executive committees of both the AFC and CAF and is the timing of the announcement, prior to a presidential election, acceptable?
"Now more than ever, this apparent exploitation of confederation resources shows the world that the actions of individuals must stop bringing FIFA into disrepute."
Both confederations released the full details of the MOU online
, saying they had "waived confidentiality."
Among its objectives, the agreement says it aims to "promote and establish friendly relations of cooperation, both among themselves and among their Member Associations, serving the interests of football in their respective territories and complying with the statutes of AFC, CAF and FIFA."
Issa Hayatou, president of the African Football Confederation (CAF) and interim head of FIFA, said the agreement was an extension of the close relations between the two regions.
"We have had various exchange partnerships bound us in the past, especially as concerns our officials for major competitions, and even very high-level matches between teams from our two confederations," he said in Kigali on Friday.
"Today, it is all about resuming a mutually beneficial cooperation between two continents with lots of similarities, and having the same challenges as concerns the development of football.
"We strongly hope that the first four years of the execution of this memo of understanding will consolidate our ties, intensify our cooperation, and build the capacities of the various stakeholders of football in Asia and in Africa."