Founded in 2016 in Nigeria, the San Francisco-headquartered firm, specialises in individual and consumer transfers, one of several fintech firms facilitating and capitalising on Africa's booming payments market.
Earlier this year, the firm raised $250m, valuing the startup at more than $3bn.
Kenya's Assets Recovery Agency sought and was granted a High Court order to freeze several accounts with three banks belonging to Kenyan-registered Flutterwave Payment Technology Ltd.
Flutterwave confirmed it owned the company.
It said in a separate statement that claims of financial impropriety in Kenya were "entirely false".
The court order, which is dated July 1, stops Flutterwave from any transactions from more than a dozen accounts with three banks, which held $43m in dollars, sterling, euro and Kenyan shillings.
"These orders shall subsist for a period of 90 days as provided in section 84 of Proceeds of Crime and Anti-Money Laundering Act," Judge Esther Maina said in a ruling pending a full hearing and final order at a later date.
Flutterwave said its operations were regularly audited and it continuously engaged regulatory agencies to stay compliant.
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