Three former FIFA officials, including ex-president Sepp Blatter, conducted a "co-ordinated effort to enrich themselves" which cost the organisation more than €70million (£55million) in the last five years.
Football's world governing body announced that Blatter, former secretary general Jerome Valcke and former deputy secretary general Markus Kattner, who also served as FIFA's chief financial officer, received the compensation awards from 2011 to 2015.
The disclosure came as part of an update into the investigation of wrongdoing at FIFA, which is being conducted by attorneys Quinn Emanuel.
"The evidence appears to reveal a co-ordinated effort by three former top officials of FIFA to enrich themselves through annual salary increases, World Cup bonuses and other incentives totalling more than 79m Swiss francs - in just the last five years," said Bill Burck, a partner with Quinn Emanuel.
FIFA made the announcement on the day Swiss authorities revealed the organisation's headquarters were searched by law enforcement officials.
The Office of the Attorney General of Switzerland (OAG) conducted the search and seized documents and electronic data as part of its probe which initially began into the circumstances surrounding the bidding for the 2018 and 2022 World Cups.
A statement from the OAG read: "As part of the ongoing criminal investigations in the FIFA affair, the Office of the Attorney General of Switzerland (OAG) carried out a search of FIFA's headquarters on June 2, 2016 with the aim of confirming existing findings and obtaining further information.
"Documents and electronic data were seized and will now be examined to determine their relevance to the ongoing proceedings.
"The investigations still relate only to the persons named in earlier statements issued by the OAG and further persons unknown. As proceedings are ongoing, no further information can be given at present."
Blatter is one of the individuals subject to the Swiss authorities' criminal investigation over the "disloyal payment" of 2million Swiss francs (just under £1.4m at current exchange rates) that was made to ex-UEFA president Michel Platini in 2011.
The criminal case is ongoing but both have been banned from all football activity over the payment by FIFA's ethics committee.
The Court of Arbitration for Sport (CAS) reduced Platini's ban to four years on appeal, while Blatter's ban has been reduced from eight to six years by FIFA's own appeals committee.
CAS is still to give its ruling on Blatter's appeal to the court.
The offices of European football's governing body UEFA were raided in April by Swiss police following the Panama Papers leak.
Some of the documents appeared to show that current FIFA president Gianni Infantino had signed off on a Champions League television rights deal in 2006 which is under investigation by the US Department of Justice.
Infantino, who at the time was UEFA's director of legal services, has denied any wrongdoing in relation to the documents.
The Swiss police investigation is also looking at Blatter in regard to whether other TV rights were deliberately undersold during his reign as president.
The home of Valcke, who was banned from football for 12 years in February, was also raided by Swiss police in March and he was questioned on suspicion of "various acts of criminal mismanagement".