Earthquake Commission chief executive Ian Simpson, who led the organisation through the aftermath of Canterbury earthquakes, has quit the role.

The commission said Simpson was stepping down at the end of the year to become head of another Government agency, GNS Science.

Simpson took on the role in 2010, before two major quakes struck Canterbury.

Commission Minister Gerry Brownlee said Simpson had supervised one of the biggest insurance company responses to any natural disaster anywhere in the world.

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He had shown great dedication and commitment to the role over the past six years, Brownlee said, despite facing "considerable, but equally undue criticism".

"From my perspective, Ian should be very proud of, and congratulated for, his leadership through extraordinary - and I hope never-to-be-repeated - times in New Zealand," Brownlee said.

EQC chairman Sir Maarten Wevers said Simpson's leadership during the commission's most challenging period had been "outstanding".

"As so many others did, he stepped up as a leader to deal with the very difficult circumstances of the time," Sir Maarten said.

During Simpson's time in charge, the EQC's staff grew from 22 people to 1800 people.

It settled 720,000 domestic insurance claims and managed the repair of 68,000 homes.

The commission also faced heavy criticism from some Christchurch homeowners who said it had been too slow, or unfair, in responding to claims.

Before joining the EQC, Simpson held a senior role at the Accident Compensation Corporation and worked for various businesses including British Petroleum (BP).