The chairman of disaster recovery specialist Guardian iT resigned after the company found a discrepancy of up to £2.5m in its accounts.
Richard Raworth said his decision to quit was a "matter of principle".
The value of the company's stock has been decimated over the past two months.
It slumped 46% to 41p on Tuesday after the announcement the company was bringing in KPMG for an independent forensic accountancy investigation.
The shares had been trading at 450p in December.
The shares crashed to nearly half their value when on
17 December the company revised its forecasts and announced it would have a net loss of £110m.
That announcement came just three weeks into the job for new finance director, Neal Roberts, who replaced Peter Jakob.
The plummeting share price reflects nervousness among investors over accounting problems following the Enron bankruptcy.
Raworth said: "I very much regret the company has had to make a second accounting-related announcement in a short space of time. In the circumstances I felt a senior resignation from the board was appropriate.
"Given my view of the crucial importance of Peter MacLean to this business in his role as chief executive, particularly in these challenging times, I felt it right I should offer my own resignation."
He stressed in a statement that neither he nor any other members of the board had been aware of the problems.
The statement did not reveal the nature of the discrepancy nor how the problem was discovered.