Cuomo filed a motion seeking the testimony after Thain refused during a deposition last week to disclose information on bonuses paid to individual Merrill Lynch employees in 2008, the Financial Times reported Monday.
"I don't want to have him sued by the company for their saying he's violating someone's privacy," Thain's attorney, Andrew Levander, told prosecutors.
Cuomo said in court papers Merrill Lynch set up a $3.6 billion bonus pool Dec. 8, and then did not adjust the amount accordingly as the company's pre-tax operating losses topped estimates by $7 billion, the Financial Times reported. Fourth quarter pre-tax operating losses amounted to $21 billion.
After the newspaper reported on the bonuses in January, Bank of America Corp. -- which merged with Merrill Lynch in September -- said Thain was responsible for the payments. However, the Financial Times said Monday evidence has developed suggesting that Bank of America Chief Executive Officer and President Ken Lewis and members of his merger transition team knew much more about the bonuses than they had acknowledged.
Thain resigned from Bank of America in January.