Ranking revisions that make Frankel the top-rated horse in history but downgrade others are bizarre, says Shergar's ex-jockey Walter Swinburn.
Frankel was promoted after ratings for previous best Dancing Brave, and other horses including Shergar, were cut.
"I find the whole thing baffling. Trying to rewrite history is not the way to go," Swinburn told BBC Sport.
But senior handicapper Phil Smith, who helped draft the changes, said it made comparisons between generations fairer.
The rating for unbeaten retired champion Frankel was confirmed as 140 on Tuesday, but Dancing Brave is now 138 - down from 141 - following a "historical recalibration" of Flat racing's international rankings, which started in 1977.
A review of the World Thoroughbred Rankings said handicapping methods - which determine a horse's mark - had ''evolved'' over the past 35 years and that top horses from the 1970s and 1980s had elevated figures compared with those they would achieve today, leading to several ratings that have stood for years being revised.
"They could have made this simple and given Frankel a higher rating if needed and left the others where they were," said Swinburn.
But Smith responded: "To fiddle it just to get Frankel on a higher mark would be wrong. This wasn't an exercise to make him the best horse.
"We thought it was best to be honest and say the system has changed, the methodology is different.
"A whole host of horses have been readjusted so, with reasonable certainty, we can compare horses from different generations."
The 1981 Epsom Derby winner Shergar and dual 1970s Prix de l'Arc de Triomphe winner Alleged, who were joint second on 140 with Frankel, are now down to 136 and 134.
The ratings are expressed in the equivalent of pounds in weight. So according to the rankings, Frankel - who was retired to stud in October after 14 wins - would be 2lb superior to 1986 Arc victor Dancing Brave.
"I find it all rather bizarre, dropping a horse 4lb from 30 years ago. I don't really understand it," said Swinburn.
"Everyone is on a Frankel high and obviously the handicappers still are. I'm sure everyone has been swept along with that."
Frankel, trained by Sir Henry Cecil, and owned by Prince Khalid Abdulla, ended his career with victory in the Champion Stakes at Ascot.
He was retired aged four for a breeding career, due to start in February, where he commands a stud fee of £125,000 a time.
Dancing Brave, also owned by Abdulla and trained by Guy Harwood, won eight of his 10 races in 1985 and 1986 - including the 2000 Guineas, Eclipse, King George VI and Queen Elizabeth Stakes and the Arc.
"Even though I rode Shergar, I would say Dancing Brave is the one that has been really hard done by. To my mind Dancing Brave was a really exceptional horse. They could have left them together," said Swinburn.
Frankel, who won the 2000 Guineas but did not run in the Derby or Arc, earned his highest rating twice during 2012 - in the Queen Anne Stakes at Royal Ascot and York's Juddmonte International.
Smith said changes to the system, which now covers 15 countries, had been in the pipeline for four years.
When the rankings started in 1977, only Britain, France and the Republic of Ireland took part and 145 horses were rated 120 or above, compared with just 18 in 2004. The average rating of the top 20 horses had dropped from 132 to 122 during that period.
"We are not saying they got it wrong. It would just be done differently now," added Smith.
Teddy Grimthorpe, racing manager to Abdulla, said he was delighted Frankel topped the ratings.
"Of course everyone has individual opinions, that's the beauty of horse racing. We are particularly biased about Frankel, but he's the best I've seen, no question," he said.