Alan Schofield worked as a special adviser between 2004 and 2006, while Prescott was Deputy Prime Minister.
Private investigator Glenn Mulcaire is understood to have hacked Schofield's phone in 2006, while investigating Prescott's affair with Tracey Temple.
PRWeek has learned that the Metropolitan Police told Schofield earlier this year that he had been hacked, after analysing Mulcaire's notes and phone records.
He has since taken on law firm Bindmans in his case against News International.
The news follows revelations that private investigators working for News International targeted Prescott's other former political adviser, Joan Hammell.
Tony Blair's former media adviser, Alastair Campbell, and Tessa Jowell's ex-adviser, Bill Bush, have also been hacked.
After leaving the Cabinet Office, Schofield worked as a director at Bell Pottinger and as deputy political editor at The Sunday Times.