The Central Office of Information wants to find out if government websites are offering value for money.
All central government departments will be required to provide their usage figures for audit.
COI has appointed ABCe, as a sole third party, to independently validate the figures generated by the audit.
And once the figures are collated the COI will publish comprehensive figures on the cost, quality and use of government websites by June 2010.
COI board director for interactive services, Alex Butler, said, "We are determined to drive up the quality of government websites to ensure they offer excellent value for money for the taxpayer, and a better user experience.
"COI has a key role to play in ensuring government can connect effectively with citizens and business online."
The audit is, in part, a response to a Public Accounts Committee recommendation for reliable data on the volume and use of central government sites. It is also being driven by a desire for COI to provide greater accountability for its own investment in digital media.
Butler said that a consistent set of measurements for unique users/browsers, page impressions, visits and durations of time spent on sites will "underpin the audit".
"These industry-agreed standards will, for the first time, accurately assess how much central government sites are being used," he said.
COI's framework for measuring cost effectiveness and performance of websites can be found at www.coi.gov.uk/webguidelines