Trinidad and Tobago's soccer federation said Warner, its former special adviser, controlled a bank account in its name that was set to receive $750,000 pledged by FIFA and South Korean soccer leader Chung Mong-joon toward soccer rebuilding projects.
Haitian officials told The Sunday Times in Britain that they have received only $60,000, and FIFA said it has frozen all funding to Trinidad and Tobago until it gets answers.
The TTFF acknowledged it had ''surrendered its authority'' to Warner, who headed soccer's North and Central American and Caribbean governing body for almost 30 years until he resigned last year to avoid a bribery probe.
''The current executive is unaware of how these funds were disbursed or utilized and is awaiting the promised audited accounts from Mr. Warner,'' the federation said in a statement. ''Sadly, Mr. Warner seems disinclined to comply with our repeated requests.''
Requests seeking comment from Warner and his lawyer in Trinidad, Om Lalla, were not returned Thursday.
FIFA cannot discipline Warner - who is a minister in Trinidad's government - while he remains in exile from world soccer. FIFA said it is withholding pension payments Warner was due to start receiving in January.
FIFA can also threaten to suspend the TTFF.
Warner's unconventional financial relationship with the federation has been detailed in Trinidad's High Court, where 13 players from the island's 2006 World Cup team are still fighting to receive millions of dollars in bonuses they claim he promised but never paid.
Earlier this month, team veterans joined authorities in seizing office equipment from the TTFF's offices due to the payment dispute.
In court on Tuesday, Judge Devindra Rampersad said Warner had written to him denying knowledge of any World Cup accounts. The judge adjourned the hearing to give the federation time to decide what it will do to make the overdue payment.
The TTFF said it was aware that FIFA and South Korea's soccer federation had sent money for Haiti, though it did not know how much was received. FIFA sent $250,000 at Warner's suggestion, and Chung pledged $500,000.
Warner requested that the money ''did not go into the account used by the TTFF administration for its day-to-day operations, but instead'' to a separate account, the TTFF said.
''We never questioned his authority or actions and are now in a position of despair as we are starved of funds by FIFA until full disclosure, which we are unable to provide without Mr. Warner's input,'' the TTFF statement said.
Each of FIFA's 208 national members is entitled to a $250,000 annual grant toward operating costs and can ask for further funding for specific projects.
The bribery scandal that brought down Warner emerged last May after he arranged for CFU officials to meet FIFA presidential candidate Mohamed bin Hammam in Port of Spain. Whistleblowers reported being offered $40,000 in cash in a brown envelope and FIFA banned the Qatari official for life.
A further $3 million in FIFA aid to Haiti was spent correctly after the governing body dealt directly with officials and contractors there, FIFA said this week.