The Charity Commission has been in contact with a think tank that is allegedly influential among senior Conservative pro-leave politicians about whether the charity is complying with its charitable objectives.
The commission has been "engaging with" the trustees of the Legatum Institute Foundation after concerns were raised by critics of the charity about its political agenda.
Some media reports have claimed that the charity is an influential voice among supporters of Brexit, but the charity’s website says it did not take a position in the run-up to last year’s EU referendum.
Instead, the charity has been examining the UK’s role in the world and its trade policies post-Brexit, the institute’s website says.
In a statement, the foundation said it had been "subject to a series of misleading and false allegations which risk significant harm to our work and reputation", and it had proactively contacted the Charity Commission about the allegations.
According to the Charity Commission website, the charity was registered with the regulator in 2011 to "advance the education of the public in national and international political, social and economic policy, focusing on understanding, measuring and explaining the journey from poverty to prosperity for individuals, communities and nations".
The charity’s income has grown from £2,500 in 2013 to £4.4m last year.
A spokeswoman for the Charity Commission said: "We are aware of media and parliamentary interest in the Legatum Institute Foundation, a charity with objects to promote education.
"We will be engaging with the charity’s trustees to seek assurances that they continue to comply with our guidance on the advancement of education for the public benefit and that they are actively protecting and promoting the charity’s independence."
The commission is understood to believe that the decision to register the charity was correct on the basis of the documents, information and assurances the regulator received at the time.
The charity’s statement said that the charity was sharing evidence with the regulator "to demonstrate how the activities of LIF are in line with relevant guidelines, as well as the steps we have taken to protect our independence and advance our research and educational work".
It added: "We are determinedly independent and non-partisan, and we guard our independence vigorously. We are not party political and do not promote any particular party policies; we remain open to all ideas and policies that will help move people from poverty to prosperity. We go where the evidence leads us."