Reports earlier this week alleged that Jones is being investigated by the FSA for his part in leaving 1,917 mortgages out of Northern Rock arrears data in 2006.
David Baker, former deputy chief executive at the lender, has been banned and fined £504,000 by the regulator for his role in the arrears cover-up.
Baker became aware that the data was inaccurate in 2007 but failed to escalate the issue and went on to mislead the market about the true extent of arrears on Northern Rock’s mortgage book.
Richard Barclay, Northern Rock’s former managing credit director, has been fined £140,000 and banned from holding a senior role at any FSA-regulated firm.
A statement from Northern Rock says: “Northern Rock (Asset Management) announces that David Jones, chief financial officer has left the company with immediate effect.
“This enables Mr Jones to focus on an ongoing FSA investigation into matters relating to a period before the company entered public ownership.
“The company is not subject to any sanction from the FSA as a result of this investigation.”