The amount (USD 23,000) is for legal fees and related expenses incurred, and does not include the damages for the lawsuit that have yet to be assessed by the High Court, according to media report.
Justice Lee Seiu Kin made the order in a closed-door hearing with lawyers from both sides present.
Senior Counsel Davinder Singh is the Prime Minister's lawyer, while M Ravi acts for Ngerng, report said.
"At the hearing today, the Judge ordered that the total costs to be paid by the Defendant to the Plaintiff be fixed at SGD 29,000," said Lee's press secretary in a statement.
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CPF is a compulsory monthly wage deducted contribution that eventual works as financial support after retirement.
Lee stands ready to be cross-examined, a position he has earlier communicated to the Court.
The dates for the subsequent hearings are not confirmed.