According to the UK newspaper The Sunday Times, Charles, 73, personally accepted money from Bakr and Shafiq bin Laden.
While denying some of the allegations in the article, a Clarence House spokeswoman did admit that the organisation had indeed accept the funds.
"We have confirmation from The Prince of Wales' Charitable Fund that careful due research was done before accepting this payment.
Just over a decade after bin Laden's attack on America on September 11, 2001, the transaction apparently took place on October 30, 2013, according to reports.
According to The Sunday Times, Clarence House and the Prince of Wales Charitable Fund had advised Charles not to take the money.