The Asian Football Confederation (AFC) named host nation Qatar, ranked 97th in the world, as the surprise top seeds while Japan were fifth and Australia sixth ahead of Friday's draw for the finals.
"We see no reason to follow FIFA rankings," AFC spokesman Ali Al-Hamdani said on Thursday.
"Seedings for the 2007 event were based on FIFA rankings so as to accommodate Australia, who were making their debut in the competition after moving across from Oceania to Asia. The 2007 system was a one-off to make it fair on other teams following the arrival of Australia."
With Australia, ranked 19th in the world, now an established force in the continent, the AFC has based the seedings for the January 7-29 event according to results in previous tournaments.
Champions Iraq, who had their international suspension lifted by world football's governing body FIFA last month, 2007 runners-up Saudi Arabia and South Korea make up the rest of the top four seeds.
As a result of the seedings, South Korea could face a showdown with bitter rivals North Korea in the group stages.
The 16 nations will be placed into four pools of four in the draw, which takes place on Friday at Doha's Aspire Dome - the largest indoor sports facility in the world.
While most teams will be eager to find out which groups they have been drawn in, Qatar organisers face a race against time to fill the stadiums during the state's largest international sporting event since the 2006 Asian Games, when many seats were empty.
Organisers say they can guarantee full houses at the five designated stadiums, which they hope will strengthen their chances of winning the bid to host the 2022 World Cup.
"Of course, the successful planning of the Asian Cup will have a major bearing on our World Cup bid," Qatar organising committee chief executive Saud Al Mohannadi told Reuters.
"Preparations are in full swing. We will be targeting both domestic and expat fans. We expect 70 percent of fans to be expats based and working in the region."
Fears have been raised that Doha's expensive hotel rates could put off travelling fans.
But Mohannadi said special accommodation rates and packages together with relaxed visa rules and ticketing - which will be announced after the World Cup in South Africa in June - would make the tournament affordable.
The groups will be drawn from four pots:
Pot 1 - Qatar, Iraq, Saudi Arabia, South Korea
Pot 2 - Japan, Australia, Iran, Uzbekistan
Pot 3 - China, UAE, Bahrain, Jordan
Pot 4 - Syria, Kuwait, India, North Korea
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