The south London supermodel created Fashion for Relief (FFR) in 2005 to raise funds for children living in poverty and adversity.
It says it has raised millions of pounds for good causes.
The Charity Commission said FFR had previously been subjected to a compliance investigation.
During that case, which opened in September 2020, the Commission identified a range of regulatory concerns relating to the governance and finances of the charity.
This included the charity's consistent late filing of accounts and lack of evidence to show that conflicts of interest were being managed, it said.
In March this year, the Commission issued the trustees with an action plan, aimed at improving the charity's financial management.
Following a review of the charity's response to the action plan, the regulator identified further concerns in the charity's financial management and governance to explore.
As a result, the Commission escalated its engagement with the charity to an inquiry, which will examine:
* whether those in control of the charity have properly exercised their legal duties and responsibilities under charity law
* the financial management of the charity, including payments made to a trustee for services provided to the charity and the level of charitable expenditure
* the governance and management of the charity by the trustees including the failure to file statutory returns on time
* whether there has been misconduct and/ or mismanagement by those in control of the charity
A spokesperson for FFR said it hoped to "conclude the regulatory engagement with the Commission as swiftly as possible" and added it had asked for an extension to the deadline as it had not been able to hold any events or undertake any fundraising activity for two years due to the pandemic.
"Any suggestion of wrongdoing or misconduct on the part of the trustees is untrue and denied," the statement added.
It said FFR was not solely a fundraising charity, and instead held events to help encourage donations to other charities and good causes.
"Each of our events has been held for the benefit of a third party charity. At each event, all donations and pledges are made directly to the third party charity," it said.