The president of The La Fondation du Prince has resigned due to concerns about a possible "activity ofthugs "linked to the educational charity of the future king.
Douglas Connell said he would be responsible " if it appears that a serious fault could have been committed ".
Newspaper articles alleged the charity had accepted £ 100,000 from a Russian donor who was later promised a meeting with the Prince of Wales.
The Scottish Charity Regulator is investigating the allegations.
Charity ethics committee had ultimately rejected donation from former banker Dmitry Leus, the Mail on Sunday and the Sunday Times reported.
The chief executive of the Prince 's Foundation, Michael Fawcett, temporarily resigned earlier this month, following separate allegations he had offered to help secure an honor for another major foreign donor .
Mr. Connell, who as chairman oversaw the governance of the charity, said: “I am both shocked and dismayed by the press reports that dishonest activity of all kinds may have taken place at the charity. 'inside and outside the Prince's Foundation.
"I and the other members of the board of directors were not aware of any of these activities, and we launched a rigorous investigation andindependent.
"My point of view is that the person who chairs the organization must take responsibility if it appears that a serious fault could have been committed within him.
"I think the right course is for the president to accept this responsibility and step down from the role.
Another charity executive, Development Director Chris Martin, has also temporarily resigned.
'Ethical Standards '
A representative of the Prince 's Foundation - which provides education and training programs across the world - said : "The Prince Foundation understands and respects Mr. Connell's decision to step down.
" We would like to thank him for all of his work to date and wish him good luck.
"The The Prince's Foundation takes the allegations made in recent press articles very seriously and is committed to upholding the highest ethical standards.
"These changes toThe board of directors will not affect the scope or timing of the rigorous independent investigation already underway. "
Prince Charles is chairman of the foundation but not involved in its governance. The directors of the association oversee its daily activities.
An investigation has been launched into the allegations relating to Mr. Fawcett, by an independent team on behalf of the directors of the foundation.
A spokesperson for Clarence House said of this investigation: "The Prince of Wales fully supports the ongoing investigation at the foundation.