President Isha Johansen, vice president Brima Kamara and secretary general Christopher Kamara were all taken into custody by the Anti-Corruption Commission, officials said.
The head of the commission, Ady Macauley, told Reuters that he ordered the arrests after the officials "failed to answer to our repeated requests to report to us for an investigation into discrepancies in the financial statements of the SLFA."
He said the investigations related to "donor funds" from the world governing body, FIFA, but did not give any further detail.
The SLFA could not be reached on Wednesday night. Lawyers for the arrested officials were also not available to comment.
The three were picked up late on Wednesday by anti-graft officials and taken to their headquarters which was cordoned off by armed police. They were later sent to a police station in central Freetown.
Chief Superintendent Mohamed Kamara at the police station where they were being held confirmed that the Anti-Corruption Commission had handed the officials over to their custody. He said they would spend the night there.
Johansen is one of the only women in the world to head a national football federation.
Some of her family members who spoke to Reuters at the police station said her health was deteriorating and wanted her moved to a hospital.
She was voted president in August 2013. Her tenure has been filled with challenges. She struggled to find support among the football community and faced a ban on games during the Ebola outbreak, which was taking a firm hold just as she took over as president.
(Reporting By Umaru Fofana, Writing by Edward McAllister; Editing by Sandra Maler)
