The regulators in the Bahamas say that the seized assets are worth more than $3.5 billion.
The Securities Commission of the Bahamas said that the public assertions were based on incomplete information.
The FTX customer assets were transferred to digital wallet under the control of regulators on November 12 after FTX filed for Chapter 11.
The move was made to make sure the assets were safe after the firm went bust.
The company's bankruptcy team pushed back against the attempt to liquidate FTX Digital Markets, despite the fact that regulators and FTX had been sparring over the matter.
FTX founder and former chief executive Sam Bankman-Fried is due to be in court on Tuesday.
Bankman-Fried is facing allegations of fraud in addition to handling client funds on FTX that were suspected to be commingled with a trading firm.