Ali, FIFA vice-president for Asia, told AFP in a phone call from Cairo, where he is attending the Confederation of African Football congress, that an unfair system of patronage had taken root under Blatter.
"National associations have to feel that it's not a matter of an executive president going and supporting national associations on an ad hoc basis, but that they have their rights, they own this association and that they should get the support they need across the board in a case-by-case fashion," said the Jordanian royal.
Ali, Dutch football federation chief Michel van Praag and former Portugal winger Luis Figo are all vying to unseat 79-year-old Blatter, who will seek a fifth term in office in the May 29 election in Zurich.
Ali's manifesto contains several thinly veiled swipes at Blatter, including claims national associations have become dependent on his "personal approval" and a charge that World Cup revenues have been distributed "at the whim of the FIFA president".
He also warns that "drastic action" is required to restore the world governing body's credibility following corruption allegations over the decision to award the 2018 and 2022 World Cups to Russia and Qatar respectively.
When he launched his campaign in February, Ali spoke of a "culture of intimidation" within FIFA and he believes the fear of losing favour may yet influence national association representatives when they vote in the election.
"Obviously there is that fear. I have to be honest about that," he said.
"The reason being is that many national associations around the world really depend specifically on FIFA funding, even though I don't believe it's where it should be in any case.
"Their fear is that there may be punishments in that respect even down to confederations levels, where all of a sudden things are not going very well for them."
Ali, president of the Jordanian Football Association, added: "When it comes down to the election, we also need to discuss with the electoral committee how things are conducted, that it's a proper, secret ballot.
"I do have my concerns about the system that's in place right now, where possibly people could know who the voter is at the end of the day."
Figo's manifesto included proposals to increase the size of the World Cup to up to 48 teams, but Ali, 39, believes that all stakeholders should be consulted before any changes are brought in.
"I'm a bit surprised because promises are being made to increase the number of participating countries in the World Cup and at the same time, in 2022, to shorten the actual time of the World Cup," he said.
"To me it doesn't seem like there's a practical study of how things should be done and we owe it to the whole footballing world to do things in a responsible manner."
The 14-page manifesto outlines Ali's vision for a "virtuous circle of development, football and commercial success supported by a FIFA that is a service organisation and a model of good governance".
His proposals include increased investment in women's and youth football, as well as a pledge that every member association will have "a national stadium worthy of that title".
He also wants to overhaul FIFA's international ranking system, describing it as "flawed", and calls for "a full and open debate" on the introduction of video technology.
Blatter is the overwhelming favourite to win the election, but Ali said he was not yet thinking of withdrawing from the race in order to throw his support behind Van Praag or Figo.
"I can't predict what will happen before May 29 and I'm just focused on national associations, on talking to them, on learning from them and if I'm elected president, on delivering on the promises made," he said.
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