However it has not agreed to another change, requested by the charity, which would have removed the health secretary's power to transfer the charity's assets to another NHS charity.
The commission said that, "subject to parliamentary review", it had agreed to grant a scheme to Barts and the London Charity, one of the country’s largest NHS charities with £250m of assets, that will "remove certain powers of the Secretary of State for Health in connection with the regulation of the charity".
The health secretary has the power to appoint and dismiss trustees of all the 290 charities associated with NHS trusts, and to transfer funds between those charities. In some cases the minister may have the power to transfer the charities’ assets, through a grant, to an NHS trust.
Andrew Douglas, chief executive of Barts and the London, told Third Sector he believes the scheme will take away the health secretary’s power to appoint and dismiss his charity’s trustees. The charity will meet with the commission on Wednesday to discuss the details.
Almost two years ago, the charity’s independent trustees applied to the commission to have the health secretary’s powers removed, said Douglas.
He said the commission had provisionally agreed it would make a "section 73" scheme under the Charities Act 2011, which would prevent the health secretary hiring and firing trustees. However, the charity will not take action on the minister’s power to transfer the charity’s funds elsewhere.
Douglas said that unlike most NHS charities, where the associated trust acts as a corporate trustee, his organisation has an independent board of trustees. He said the trustees had decided to seek this particular scheme because they "decided they wanted to have independence, to be able to say no to certain things, and to have autonomy to plan their strategy".
He said the charity raised several million pounds a year from major donors but aimed to raise more. He said trustees were keen that "money raised couldn’t be removed in an asset grab by the secretary of state" and that they could tell major donors that the charity was completely independent.
Jonathan Brinsden, a partner at Bircham Dyson Bell who represented the charity, said its ability to fundraise was being stifled by the "the dead hand of the state".
He said that the Department of Health and the commission had been reluctant to recognise that an element of ministerial control would make it harder for a charity to fundraise.
"They don’t see that the aims of the health minister and the aims of a health charity might not be the same," he said. "But of course a charity focused on local healthcare might have different priorities to a minister of state."
A Charity Commission spokeswoman said: "The Barts and London Charity has applied to the commission for a scheme which, subject to parliamentary review, would remove certain powers of the Secretary of State for Health in connection with the regulation of the charity. These powers apply to all NHS charities.
"The commission has agreed, subject to certain conditions, consultation with the Department of Health and review by Parliament, to settle a scheme which would remove a more limited range of powers in connection with the appointment of trustees for the charity by the secretary of state".
A Department of Health spokesman said: "We're currently conducting a review of the way NHS charities are governed, which will take into account the specific issues that Barts has raised. We will report on this later this year.
"As the Charity Commission acknowledges, this is subject to both a parliamentary review and a consultation, which we will take part in."