The move comes after the Philippines questioned the huge number of obscure sports at the Myanmar games which seem designed to ensure that the host countries and its allies reap the most medals.
The Philippine Olympic Committee in a statement said it had sent a letter asking that Filipina swimmer Jasmine Alkhaldi be given back her gold.
Alkhaldi, 20, won the 100 metre freestyle on Thursday, but it was quickly taken back after Thailand protested, saying there had been a "false start."
A re-swim was then ordered the following day, in which Alkhaldi came in third behind athletes from Thailand and Singapore, respectively.
A member of the Philippines' SEA Games task force said the "re-swim" had put the Filipina at a disadvantage.
"You cannot regain that adrenaline from the first final swim. The momentum of our athletes was diminished," said task force member Paul Ycasas.
The head of the Philippine mission to the Myanmar games Jeff Tamayo also said the order for a "re-swim" did not follow the rules set up by FINA (International Swimming Federation), the sport's governing body.
"The settlement of Thailand's protest by calling for a re-swim is simply out of order," Tamayo said in a statement.
The Philippines' head swimming coach, Carlos Brosas also charged that Singaporeans who dominate the region's swimming federation, had favoured the "re-swim" and had already advised him that the Philippines' protest would be unsuccessful.
"The guys that really run the show, the bigwigs so to speak, are Singaporeans," Brosas said in a statement from Myanmar.
He said Friday's "re-swim" had benefitted the Singaporeans as well which may explain why they favoured it.
The Philippines lags at seventh in the medal tally at the 27th SEA Games with only 10 golds so far, said Ycasas.
The country had dispatched a contingent of only 210 to Myanmar, one of its smallest ever to the competition, due to the large number of obscure games and the removal of more popular sports.
Philippine sports officials had previously considered sending only a "token" group or even boycotting the Myanmar games entirely.