Mr Warner visited the country in the months after the disaster and pledged $974,550 from football’s world governing body and the South Korean Football Association to help rebuild the country.
But US investigators said it was transferred to accounts controlled by Mr Warner for his personal use, and that four years on, the money was still unaccounted for.
A source close to the investigation told the BBC that they were working through 75 bank accounts connected to Mr Warner, but admitted some of the missing millions may never be found.
Another anonymous source said “was the most powerful man in the Caribbean”.
“Given Warner’s power in Trinidad, he could get transactions done that a regular person would not,” he said.
The attorney-general in Mr Warner’s native Trinidad and Tobago, Garvin Nicholas, has also promised to investigate.
“I think if Jack Warner actually stole money that was meant for Haiti, that is a most despicable crime, and I would expect the authorities to do all that they can to ensure the recovery of that money,” he said.
Mr Warner is wanted in the US on charges of corruption and money laundering, but denies all allegations.
He has emerged as a key figure in the scandal that erupted last month as one of 14 current or former FIFA officials and sports marketing executives accused by US prosecutors of taking part in a sweeping kickbacks scheme going back 20 years involving a total of $197 million in bribes.
The scandal, which also involves a Swiss probe into the awarding of the 2018 and 2022 World Cups to Russia and Qatar, led to the announcement of the resignation of veteran FIFA boss Sepp Blatter, just four days after his re-election for a fifth successive term.
Warner has also been accused of asking Egypt for a $US7 million bribe for votes to host the 2010 World Cup, and the BBC claimed he pocketed a $13 million payment made by South Africa through FIFA which was intended to pay for football development for the African diaspora in the Caribbean.