Khan, who was appointed to the role internally in August last year, will be replaced as CFO by Emma Mercer, who has been with the company since 2008.
An ICAEW member, Khan joined the company in 2011 from Associated British Ports.
Lee Watson, who is also a chartered accountant and ICAEW member, has also been appointed as chief transformation officer on secondment from EY, where he has been a partner since 2008.
In July it was announced that the Big Four firm was to be brought in to help the company to review its finances.
These writedowns came to light after auditors KPMG reviewd more than 50 contracts, finding four that were problematic – three large public private partnership contracts in the UK accounted for £375m and one in the Middle East for £470m.
Alongside the announcement of Khan’s resignation, the company announced four other resignations.
Chief operating officer Richard Howson, managing director of Carillion Construction Services Adam Green and managing director of Carillion Services Nigel Taylor are leaving the company on 30 September. Group strategy director Shaun Carter will leave by the end of the year.