Northern Rock Asset Management – the "bad bank" created when the lender was split in two by the UK government – said David Jones had quit with immediate effect "to focus on an ongoing Financial Services Authority investigation into matters relating to a period before the company entered public ownership".
Northern Rock stressed that it was "not subject to any sanction from the FSA as a result of this investigation".
It is believed the regulator is investigating Jones in relation to a recent inquiry into misleading mortgage arrears figures at the lender, which last week resulted in a near-record fine for its former deputy chief executive.
Details of the FSA investigation emerged when David Baker, a former deputy chief executive, was fined 504,000 and banned from working in any regulated activity after the watchdog found that he misled shareholders and analysts by quoting inaccurate data.
The fine is believed to be the highest ever for this type of offence and one of the largest handed to an individual.
A 140,000 fine was also handed to Northern Rock's former managing credit director Richard Barclay for failing to ensure the figures' accuracy.
Northern Rock collapsed into public ownership in early 2008 after it was forced to seek emergency funding from the Bank of England and suffered the first run on a UK bank for 150 years.
The bank has now been split into "good" and "bad" banks. The former contains 10.3 billion of the mortgage book and 19bn in retail savings and is set to return to the private sector.
The latter is the asset management arm, which holds about 50bn of mortgages and unsecured loans of 3.9bn. This business also holds the UK government loan and does not offer any new mortgage lending.