"Mr Ractliffe regrets his omission to inform the chairperson, chief executive officer and the rest of the board of trustees of the NMCF of his receipt of the uncut diamonds until now," the charity's board said in a statement.
Ractliffe "acknowledges that had he done so, he and the board would have found a better and lawful way to manage the situation", the statement said, adding that he had apologised for causing "possible reputational risk" to the charity.
Campbell had earlier this month told the court how she received a pouch of "dirty-looking stones" after attending a dinner with Taylor.
She told judges she gave the three uncut diamonds to Ractliffe, then the chief executive of the charity, to "do something good with".
The day after her testimony, Ractliffe confirmed keeping the stones and had never given them to the charity, saying he did not want to involve the organisation in any possible illegal activities.
He then handed the diamonds over to South African police, who have opened an investigation into the possession of uncut diamonds without a licence.
Taylor, 62, is accused of receiving so-called blood diamonds in return for arming rebels who murdered, raped, maimed and enslaved civilians during the 1991-2001 civil war in neighbouring Sierra Leone that by some estimates claimed up to 250,000 lives.