In a 5-2 ruling, the justices said eliminating the agency would take an act of the Legislature, which established the council in 1985 to be independent.
Affordable housing advocates say the ruling ensures that affordable housing policy decisions will be made by an independent board that takes input from the public.
"It's a bad idea for policies involving homes for working families, people with special needs and lower-income seniors to be made behind closed doors," said Adam Gordon, the Fair Share Housing Center lawyer who argued the case before the court.
For now, the housing council remains intact.
"If the Governor and the Legislature wish to abolish COAH, they must take another path," Chief Justice Stuart Rabner wrote in a majority opinion.
The 12-member bipartisan council was created to enforce a series of state Supreme Court rulings that found New Jersey towns have an obligation to provide housing for low- and moderate-income residents.
While progressives hold up those earlier rulings as landmarks to advance fairness to the poor in wealthy suburbs, they are also seen by some as meddlesome social engineering. And the council, which establishes and enforces rules about how much housing each town should provide, is a major target for criticism from local officials.
In a dissenting opinion, Justice Anne Patterson, a Christie appointee, noted that other governors have taken similar actions to reassign functions of independent agencies and that the Legislature did not object to Christie's action in this case. Justice Helen Hoens, named to the court by former Democratic Gov. Jon Corzine, joined the dissent.
The Republican governor cast the lack of objection from either the Senate or Assembly as tantamount to both branches approving the plan to eliminate the council.
"Not surprisingly, this liberal Supreme Court once again ignores that and continues to blindly perpetuate its failed social experiment in housing. The Chief Justice's activist opinion arrogantly bolsters another of the failures he and his colleagues have foisted on New Jersey taxpayers," he said.
"This only steels my determination to continue to fight to bring common sense back to New Jersey's judiciary," said Christie, who has previously tangled with the court, which now has two temporary justices because of political battles over filling the jobs.
Rabner, the target of Christie's anger Wednesday, will be up for reappointment next year.
A task force commissioned by Christie called the housing council "irrevocably broken." In 2011, the governor abolished COAH and gave its duties to the state Department of Community Affairs, whose commissioner reports to the governor.
Fair Share Housing Center sued, arguing that the governor's broad authority to reorganize government did not extend to agencies established to be independent. The court agreed.
"The current statute reflects careful judgments about who should make decisions on affordable housing policy and how those decisions are to be reached," Rabner wrote.
Two other legal disputes remain over COAH.
Fair Share Housing Center has also asked the Supreme Court to make the agency issue its latest round of rules on communities' housing obligations.
Also, an appeals court earlier this year said that the state had to follow a process to seize unused affordable housing money set aside by towns, but that issue is still being appealed.