Judge Andrew Napolitano said Tuesday on "The Kelly File" and on Fox Business Network that a new federal court ruling could actually delay President Obama's immigration amnesty "forever."

Napolitano explained the meaning behind the new ruling that temporarily blocks the implementation of Obama's executive actions on immigration.

The ruling came late Monday after 26 states asked the court to delay the implementation until after the conclusion of a lawsuit challenging the legality of Obama's orders.

U.S. District Judge Andrew Hanen granted the preliminary injunction Monday after hearing arguments in Brownsville, Texas, last month. He wrote in a memorandum accompanying his order that the lawsuit should go forward and that without a preliminary injunction the states will "suffer irreparable harm in this case."

"The genie would be impossible to put back into the bottle," he wrote, adding that he agreed with the plaintiffs' argument that legalizing the presence of millions of people is a "virtually irreversible" action.

The first of Obama's orders -- to expand a program that protects young immigrants from deportation if they were brought to the U.S. illegally as children -- was set to start taking effect Wednesday. The other major part of Obama's order, which extends deportation protections to parents of U.S. citizens and permanent residents who have been in the country for some years, was not expected to begin until May 19.

Napolitano called Hanen's ruling "rare," saying one federal judge usually does not decide to stop the president from doing something. He said it's more common for a federal judge to let an appeals court decide. 

"You could count on one hand the number of times a single federal judge has done this to a President of the United States since World War II and you would not use all your fingers," he said.

On "The Kelly File" Tuesday night, Megyn Kelly agreed that it was "incredible" for a federal judge to step in like this and halt parts of the amnesty program.

"It's very hard to get temporary relief like these 26 states got. Normally they'll say, 'we'll hear you out on the merits later.' But they convinced this judge that if he did not stop this executive order, there was going to be irreparable harm, that there was no way to put the genie back in the bottle," she said.

Napolitano pointed out that the judge believed the government was "disingenuous" for claiming that they had not changed federal law.

"He ruled that they were changing the law and that they violated federal law in the manner in which they changed federal law. They didn't have a 30-day waiting period, they didn't give Congress the opportunity to weigh in, they didn't let the public weigh in, they didn't publish their rules early enough. They just changed, changed, changed like the president said he would with a phone and a pen," said Napolitano.

The case now moves to the Fifth Circuit Court of Appeals that covers New Orleans and Houston, with Napolitano noting that circuit is the "most conservative" in the nation.

The judge predicted that there is almost no chance that the Supreme Court will get involved quickly in this matter if the Fifth Circuit upholds the injunction.

Napolitano predicted that the amnesty program is on hold "probably forever" unless the appeals court unexpectedly decides to overturn Hanen's injunction.

He said it will probably take longer than two years - Obama's remaining time in office - for the overall case to wind its way through the courts.

"The judge said the feds will probably lose and there is probably irreparable harm to the states, therefore I am going to stop this from happening and I'm going to stop it right now," he explained.

Watch the judge's appearance on "The Kelly File" above and his sit-down with Stuart Varney below.