Gov.uk is designed to reduce the different number of sites that people need to visit and will include information and links on a wide range of subjects, including information from non-departmental government bodies.
The commission, however, is keen to stay separate from the site, which exists in beta form and is expected to be fully operational in October, in order to maintain its independence from government.
Dame Suzi Leather, chair of the Charity Commission, told Third Sector: "The risk is that people would perceive us to be part of government and not independent at all."
A commission spokeswoman said: "In accordance with a process set out by the Government Digital Service, the Charity Commission has applied to be exempt from transition to the new Gov.uk website.
"Our submission was based on our need to be independent from the government and ministers in order to fulfil the Charity Commission’s statutory remit as the independent regulator of charities in England and Wales."
A spokesman for the Cabinet Office confirmed that the commission had put in a bid for an exemption but was unable to clarify when a decision is expected.
He said the department was "working with colleagues across Whitehall to put government information on to Gov.uk – a new shared platform where departments and related organisations can publish information about themselves and their activities, which they currently publish on their corporate websites".
"Our aim is to deliver simpler, clearer, faster services for users, and savings and innovation for government," he said.