Sheikh Salman, South African politician and businessman Tokyo Sexwale and Prince Ali are among five candidates standing in the election, with the Jordanian fearing vote deals had been struck between the two confederations who will have a combined 100 votes in the 209-member poll.
"The timing of this MOU (memorandum of understanding)between the AFC and the CAF looks like a blatant attempt to engineer a bloc vote," Prince Ali said in a statement.
"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?"
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Sheikh Salman's campaign issued a statement describing Ali's complaint as "an unnecessary spat between FIFA candidates".
The statement pointed out that the AFC has similar MOU agreements with a number of other bodies including Europe's UEFA and North and Central American confederation CONCACAF.
Salman's team said that work on the CAF MOU began long before the election campaign.
"Sheikh Salman decided to join the FIFA presidential race as late as October last year, more than five months after the CAF negotiations had started in Zurich," said the statement.
Salman said: "I am astonished about my friend's comments which are wholly dismissed and entirely inaccurate," he said.
A spokesman for FIFA's ad-hoc election committee confirmed the complaint had been received and said it would now be analysed.
Ali's team did not state which specific FIFA electoral rule they believe Salman may have broken.
Former FIFA official Jerome Champagne and UEFA general secretary Gianni Infantino are also standing in next month's election which will go ahead with FIFA mired in the worst corruption scandal in its history. Criminal investigations are under way in the United States and Switzerland.
FIFA's own ethics committee has sanctioned a number of officials, the most notable being FIFA president Sepp Blatter and European football boss Michel Platini who were both banned for eight years. Both deny wrongdoing.
The 40-year-old Jordanian royal, who was beaten by 133-73 votes by Blatter in the last FIFA presidential election in May, published his election manifesto earlier this month calling for more transparency at FIFA and term limits for senior officials.
He said FIFA faces a "catastrophic" future if the wrong man is elected.
(Writing by Patrick Johnston in Singapore and Simon Evans in Miami; Editing by Peter Rutherford and Stephen Powell)
