Football's governing body said that the money had been sent to the TTFF in 2010 at the request of former executive committee member Jack Warner, who was head of CONCACAF, the North, Central American and Caribbean (CONCACAF) Confederation, at the time.
FIFA said in a statement sent to Reuters that $250,000 was wired to the TTFF but the Haiti federation said it had only received $60,000.
Football's governing body said it still has not received "a satisfactory response" about what happened to the remaining $190,000 and has stopped further payments to the Trinidad federation.
"We can confirm that FIFA wired immediately after the devastating earthquake $250,000 as an emergency aid for Haiti to the account of the Trinidad and Tobago Football Federation (TTFF)," said the statement.
"This was on request of the then CONCACAF President Jack Warner and subsequently transferred to the TTFF account, in order to immediately provide support to Haiti.
"FIFA can also confirm that it had been informed by the Haiti Football Association (FHF) in autumn 2011 that it had only received USD 60,000 of this emergency aid.
"Consequently FIFA, in a letter, requested in October 2011 a full explanation from the TTFF into those funds.
"As FIFA has not received any satisfactory response, FIFA has stopped with immediate effect any payments to the TTFF until it will receive proper accounts of these funds allocated as an immediate relief support to the FHF."
The 7.0-magnitude earthquake killed 300,000 people and left 1.5 million homeless in Haiti two years ago.
Warner, who often worked as a special advisor to the TTFF, was a major FIFA powerbroker until he was suspended, then resigned last June.
He quit as FIFA's ethics committee investigated his role in a cash-for-votes scandal at a meeting in Port of Spain ahead of last year's presidential election.
FIFA presidential candidate Mohamed Bin Hammam, also at the meeting, was suspended for life.
Warner is Works Minister in the Trinidad government and continues to make news, with local media reporting earlier this month that he had started a campaign to bring back hanging on the Caribbean island.
FIFA said it had allocated a further $3 million to a special Haiti fund which it controlled directly.
"The fund went towards restarting the Haitian championship and purchasing sporting equipment and various materials for the national technical centre, which was itself renovated and extended," said FIFA.
"In addition, the special projects fund was used to build the completely new FHF Headquarters on the training centre property as the old one was completely destroyed in the earthquake.
"Lastly, the Sylvio Cator Stadium in Port-au-Prince was renovated, with an artificial pitch on the principal new features as well as currently with the installation of floodlights.
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