Johansen, 51, who was elected president of the Sierra Leone Football Association unopposed on 3 August 2013, was arrested together with the FA’s Vice-President Brima Mazola Kamara and Secretary General Chris Kamara.
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 ACC announced on Wednesday the start of “Operation Thunderbolt” which aims to “rout and bring to justice” people alleged to have been involved in corrupt acts and have been under the watch of the anti-graft agency.
Johansen’s arrest came a day after returning from Ivory Coast where she attended the Leone Stars Africa Cup of Nation’s 2017 final qualifying match last Saturday at the Stade de la Paix in Bouake, Ivory Coast.
The arrested persons have been detained for alleged misappropriation of funds at the CID headquarter in Freetown.
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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.