He will be replaced, on 1 November, by John Womersley, the STFC’s current director of science programmes.
Professor Mason, has been seconded to the UK Space Agency until 31 March 2012, the date on which his term at the STFC was due to end.
He was heavily criticised in a report by the Commons Science and Technology Committee into astronomy and particle physics, published in May.
The committee said his “leadership vacuum” and perceived failure to communicate effectively with the academic community had contributed to relations between researchers and the research council that were “sometimes bordering on the adversarial”.
Professor Mason will advise the UK Space Agency on the “steps needed to leverage the research base to maximise the economic growth of the space sector”.
He said: “I am passionate about the scientific and commercial opportunities that space offers, and am excited by the minister’s invitation to make an important contribution to delivering key aspects of the space innovation and growth strategy.”
Professor Womersley has been appointed for four years.
Prior to becoming the STFC’s director of science programmes in 2007, he was director of particle physics at the Rutherford Appleton laboratory at Harwell in Oxfordshire.
He has also held various positions in the US, including at the Superconducting Supercollider in Texas, Fermilab in Illinois and the US government’s Office of High Energy Physics in Washington.
Michael Sterling, chair of the STFC, said Professor Womersley had the “experience and skills to lead the organisation through the challenges ahead and ensure that the UK continues to benefit from world-leading scientific facilities”.