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Kim Man-bok admitted to a parliamentary committee that there were undisclosed terms involved in the deal with the Afghan rebels.
He said the truth would be made public at some point.
South Korean officials had previously repeatedly denied reports that money was paid for the hostages' release.
"It's not proper for you, intelligence committee members, to ask whether a ransom was paid. I think it will serve better to leave it there for a while," Kim said, according to South Korea's Yonhap news agency.
Sun Byung-ryul, a parliamentary committee secretary, told the Associated Press that when asked whether a ransom had been paid, Kim replied: "I can't confirm that. Various things happened and they will be revealed as time passed."
Kim travelled to Afghanistan to take part in negotiations with the Taleban.
As part of the deal, Seoul said it agreed to pull its troops out of Afghanistan as scheduled by the end of the year, and to stop missionaries travelling to Afghanistan.
There have been persistent media reports alleging that a multi-million dollar ransom was paid.
Afghan officials have said a sum slightly under $1m (£500,000) was handed over.
Two of the 23 Christian aid workers were murdered by their Taleban captors. Two others were then released because of their ill health, and the others were freed after six weeks in captivity. - DDNEWS