The former FIFA vice-president from Jordan spoke out after the Liberian FA chief said he would go to the Court of Arbitration for Sport if Domenico Scala, head of FIFA's ad-hoc electoral committee, does not stand down by Thursday.
Scala is Swiss-Italian like Gianni Infantino, the UEFA general secretary who is also one of five candidates in the February 26 election to head the scandal-tainted world body.
Scala pulled out of the organisation of last year's FIFA race because he has the same nationality as Sepp Blatter.
"The suggestion by the Liberian Football Association that the head of FIFA's ad-hoc electoral committee should step down is a valid request and in keeping with the precedent set by the committee chairman exactly one year ago," Prince Ali said in a statement.
"Avoiding even the appearance of a conflict of interest is particularly important at a time when people around the world, including players and fans, are questioning FIFA's integrity and ethical standards."
Prince Ali said all 209 member associations "must have full confidence that the integrity of the election is beyond question.
"If any member association has concerns about the impartiality of the electoral process, those concerns must be respected and taken seriously."
Liberian FA chief Musa Bility wrote to Scala on Monday calling for him to stand aside over a potential "conflict of interest", the BBC reported.
"Following an unprecedented period of sustained turmoil and damage for Fifa as an institution, the fairness and integrity of the current electoral process are absolutely vital for FIFA," Bility wrote.
Bility had wanted to be in the FIFA campaign but did not pass FIFA's eligibility check. He warned Scala that if he did not receive word within three days "that you are stepping down ... with immediate effect, the Liberian FA reserves its right to challenge that decision by all available routes."
The BBC quoted a FIFA spokesman as saying there was no conflict of interest.
Apart from Prince Ali and Infantino, Asian confederation chief Sheikh Salman bin Ebrahim al-Khalifa of Bahrain, South African tycoon Tokyo Sexwale and former FIFA official Jerome Champagne of France are standing in the election.