Accused criminals could lose their right to a trial by their peers if there are fears of juries being intimidated.
The measure is in government legislation introducing sweeping reforms of the jury system, including the abandonment of unanimous jury verdicts in favour of an 11-1 verdict.
Parliament will vote on it for the first time next week.
The bill lets police seek to retry those acquitted on the most serious charges if compelling new evidence comes to light or the original trial is found to have heard tainted evidence.
A measure expected to provoke complaints from defence lawyers is the fast-tracking of committal hearings to speed up the time it takes to get to trial. Prosecutors will need to present only written evidence, and defendants will have an oral hearing only if a judge believes it necessary.
Justice Minister Phil Goff announced that prosecutors would be able to seek a trial by judge rather than jury where there was evidence that jurors had been or might be intimidated. A judge-only trial could also be sought in long and complex cases.
ACT MP Stephen Franks said there was a risk of the judge-only provision being misused. "Jury involvement has been a safeguard with unpopular law or where the jury thinks the Government is abusing prosecution power."
Warnings from the highest level say the change to double jeopardy rules breaches the Bill of Rights.
"The proposal will result in all persons who were accused and acquitted of these charges, regardless of the seriousness of the relevant circumstances surrounding the charge, having to live with the possibility of continued police investigation, renewed prosecution and other onerous consequences of exposure to the criminal justice system," Attorney-General Margaret Wilson said.
In a report to Parliament under the Bill of Rights Act, Ms Wilson said the double jeopardy rule was of "great significance and importance". "The fundamental purpose . . . is to protect individuals against the excessive use of state power. The state, with all its resources and powers, should not be allowed to continually subject an individual to repressive and repeated prosecutions."
The change to double jeopardy rules was sparked by the trial of a New Plymouth gang member who got off on a murder charge when a witness lied about vital fingerprint evidence. He could not be retried even after the witness recanted.
Ms Wilson said in cases where the courts had heard tainted evidence the accused should be retried. But the net had been cast too wide in the case of fresh and compelling evidence, covering more than 40 offences.