The Badminton World Federation (BWF) said in a statement on Wednesday that Gaya had been fined $50,000 (39,286.56 pounds) by its ethics hearing panel following an investigation that started in June last year.
The charges against Gaya stated that grants or funding intended for the Mauritius Badminton Association (MBA) had been diverted into personal bank accounts and used "for his own benefit".
He was also accused of submitting forged accounting documents and falsifying or exaggerating expenses.
The ethics hearing panel also looked into claims that money paid by the Badminton Confederation of Africa (BCA) to help shuttlers qualify for the 2016 Rio de Janeiro Olympics had been siphoned off.
"The BCA allocated $21,485 to the MBA... and paid $19,150 (to) Mr Gaya for that purpose, of which about $18,000 should have been paid to the Mauritian player Kate Foo Kune," it said.
The player declared in a witness statement that she had received only $1,100, money the BWF said was paid in cash only after the player was "forced to pester" Gaya.
The former official said in his defence, before ceasing to cooperate with the BWF investigation, that he paid more than $1,100 but some money had gone to the national association for her expenses.
The panel ordered $5,000 of the fine to be paid to the player, a multiple African women's singles champion who was the Mauritian flag bearer at the opening ceremony of the 2016 Olympics.
Gaya had held positions with the BWF, BCA and MBA since 1999.
In May the BWF banned two Malaysian players for 15 and 20 years for betting and match-fixing offences.
(Reporting by Alan Baldwin, editing by Ken Ferris)
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