U.S. District Judge Jed S. Rakoff made the conclusion in an 11-page order in which he said he was about to toss out the death penalty eligibility of two men charged in a drug and murder conspiracy.
He said an earlier ruling by the U.S. Supreme Court upholding the federal death penalty law relied on an assumption that it was "highly unlikely that an executed person would subsequently be discovered to be innocent."
"That assumption no longer seems tenable," Rakoff said, citing evidence including a recent Columbia Law School study concluding that the rate of prejudicial error in the capital punishment system was 68 percent.
"Evidence has emerged that clearly indicates that, despite all the aforementioned safeguards, innocent people - mostly of color - are convicted of capital crimes they never committed, their convictions affirmed, and their collateral remedies denied, with a frequency far greater than previously supposed," the judge wrote.
He gave the government a final opportunity to present arguments on the subject before he issues a final ruling after May 31.
"If the court were compelled to decide the issue today, it would ... grant the defendants' motion to dismiss all death penalty aspects of this case on the ground that the federal death penalty statute is unconstitutional," Rakoff wrote.
CBSNews.com Legal Analyst Andrew Cohen says even if the judge issues the final order it won't automatically impact other capital cases around the country and the government almost certainly will appeal the ruling up the appellate ladder. This is often how major constitutional changes occur in this country, however, over time, with a single judge's rationale being applied by another judge and then another.
In 1988, Congress passed the so-called "Drug Kingpin" statute that allowed prosecutors to seek death against large-scale dealers in murderous gangs.
In 1994, Congress passed the Federal Death Penalty Act, which increased the number of crimes that could result in a death sentence.
Since then, federal prosecutors have sought death against six defendants in New York State. Juries in each instance have voted to impose life sentences instead.
Attorney David Ruhnke, who represented all six defendants, did not immediately return a telephone message for comment.
Marvin Smilon, a spokesman for U.S. Attorney James B. Comey, said prosecutors had not yet received a copy of Rakoff's decision and could not immediately comment.
Oklahoma City bomber Timothy McVeigh is one of only two people nationwide who have been executed since the federal death penalty statute was revived.
Since 1988, the federal government has filed notice to seek the death penalty in 240 cases. Of those, 204 have been resolved through plea bargains, verdicts or a government decision to withdraw its request, the New York Law Journal reported in an article this week.
Currently, 20 people are on federal death rows nationwide.