He issued a statement after her testimony at the war crimes trial of ex-Liberian leader Charles Taylor.
It is alleged she received the gems from Mr Taylor in 1997, which could link him to illegal “blood diamonds”.
Ractliffe said he was happy to testify at The Hague and had now handed the stones over to the authorities.
“Three small uncut diamonds were given to me by Naomi Campbell on the Blue Train on 26 September 1997,” he said in a statement sent to the BBC.
At the trial, Campbell said she was given some “dirty-looking stones” after a 1997 charity dinner hosted by South Africa’s former President Nelson Mandela where Mr Taylor was also a guest.
She said two unidentified men appeared at her room and gave her the stones.
She told the court she did not have proof they came from Taylor and had given them to Ractliffe because she wanted the stones to go to charity.
“Naomi suggested they could be of some benefit to the Nelson Mandela Children’s Fund (NMCF) – but I told her I would not involve the NMCF in anything that could possibly be illegal,” Ractliffe said.
The fund has repeatedly denied receiving any diamonds from Campbell.
Ractliffe, who is still a trustee of the fund, said he took the diamonds as he thought it might be illegal for her to take them out of the country.
“In the end I decided I should just keep them,” he said.
“A factor that influenced me not to report the matter to anyone was to protect the reputation of the NMCF, Mr Mandela himself and Naomi Campbell, none of whom were benefiting in any way.”
The BBC’s Jonah Fisher in Johannesburg says it is not clear when Mr Ractliffe handed over the stones to the South African authorities.
Allegations that the uncut gemstones were given to Campbell emerged in a statement by US actress Mia Farrow, who also attended the 1997 dinner.
Farrow and Ms Campbell’s former agent former agent Carole White are due to appear before the Special Court for Sierra Leone at The Hague on Monday.
Taylor is accused of using illegally mined diamonds to secure weapons for Sierra Leone’s RUF rebels during the 1991-2001 civil war – a charge he denies.
Prosecutors say that from his seat of power in Liberia, Taylor also trained and commanded the rebels.
The rebels were notoriously brutal, frequently hacking off the hands and legs of civilians. BBC