Jin Lee/Bloomberg News

The first batch of checks for eligible victims of Bernard L. Madoff’s epic Ponzi scheme will go into the mail starting Wednesday, according to the trustee liquidating the Madoff estate in federal bankruptcy court.

The payment — totaling $312 million — “is the first return of stolen funds to Madoff’s defrauded customers,” the trustee, Irving H. Picard, said on Tuesday. “The need among many Madoff customers is urgent, and we are working to expedite these distributions.”

The payments would have been made last week, but were delayed for a few days to allow Mr. Picard’s lawyers to analyze the effects of a significant ruling on Sept. 27 by Judge Jed S. Rakoff of United States District Court in Manhattan in a case involving the owners of the New York Mets. In that ruling, Judge Rakoff allowed the trustee to seek only the return of fictional profits the Mets owners withdrew in the last two years of the fraud, which lasted more than a decade.

The trustee, citing New York State law, had sought to recover fictional profits paid in the six years before the scheme collapsed in December 2008. The judge also rejected the trustee’s bid to recover preference claims, the cash paid to team owners in the last 90 days of the fraud.

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If applied to the hundreds of lawsuits Mr. Picard is pursuing against other Madoff investors who withdrew more than their original cash principal, the ruling would reduce Mr. Picard’s potential recoveries by $6.2 billion.

The trustee delayed the payments last week until he could determine if the ruling would affect the proposed distribution. Those potential issues “have since been resolved,” Mr. Picard said Tuesday in a statement.

The $312 million is being distributed to the holders of 1,230 Madoff accounts and represents a recovery of roughly 4.6 cents on the dollar. The customers eligible for payouts are those who had not withdrawn all the cash they had invested. Some may have already received cash advances of as much as $500,000 from the Securities Investors Protection Corporation, an industry-financed fund that handles brokerage firm liquidations. Under a federal appeals court ruling in August, investors who recovered all their initial cash outlay before the fraud collapsed are not eligible for the current distribution.

Through out-of-court settlements by the trustee and civil forfeiture agreements with the Justice Department, $10.7 billion has been collected to cover what the trustee estimates to be about $18 billion in out-of-pocket cash losses by eligible victims — a sum that ultimately could allow those victims to recover more than half the cash they lost in the Madoff fraud, far more than is typical in Ponzi schemes.

According to the trustee, that cash — including $7.2 billion from the estate of Jeffry Picower, a longtime Madoff investor who died in 2009 — cannot be distributed until the resolution of appeals challenging the terms of those settlements and the formula Mr. Picard used to calculate eligible claims in the complex and controversial liquidation.

“While we cannot predict the timing of rulings on these appeals, we maintain that the appeals of the Picower and other settlements are frivolous and will be dismissed,” said David J. Sheehan, a lawyer for the trustee and a partner at Baker Hostetler. If the trustee prevails in those court battles, he would “distribute those funds as quickly as possible,” Mr. Sheehan said.

Mr. Picard has sued for nearly $100 billion in fictional profits and damages from giant global banks, hedge funds and investment managers who dealt with Mr. Madoff during his scheme. If the trustee recovers more than the $18 billion, the money could be used to cover general fraud claims by all Madoff investors.