"Interim arrangements will apply with the Deputy Chief Ombudsman, James Dipple-Johnstone, covering the Chief Ombudsman role and the Chief Finance and Risk Officer, Jenny Simmonds, covering the Chief Executive role," the FOS said.
Ms Thomas, who joined the FOS less than two-and-a-half years ago as chief executive and chief ombudsman, is said by insiders to have lost the confidence of the organisation's chair Baroness Manzoor.
That pressure resulted in the ousting of the Competition and Markets Authority chairman last month, and one bank executive said that Ms Thomas's exit - while not directly instigated by ministers - was a reflection of the same mood.
The head of the Financial Ombudsman Service (FOS) has effectively been forced out of the role after losing the confidence of its board amid growing government pressure on economic watchdogs.
In its statement on Thursday, the FOS - which is operationally independent but handles complaints according to rules published by the Financial Conduct Authority (FCA) - noted simply that Ms Thomas was "stepping down".
