Local communities around the Fly River filed a writ against Ok Tedi Mining Limited to stop depositing waste into the river system amid concerns over the environmental and health impacts.
PNG Prime Minister Peter O'Neil said the government would appeal the court decision, which could have "horrendous" financial, economic and social consequences.
The court also ordered the government and OTML to disclose all financial records, bank statements, and other documents.
Communities around the area have long complained about pollution, as well as a reduction in fish and wildlife, with some villages claiming the waste is responsible for deformities in children born in the area.
South Fly River community leaders lawyer Samson Jub told the ABC that the interim order was long overdue.
"The court has ordered Ok Tedi Mine Limited to stop dumping anymore mine waste and tailings into the Ok Mine, Ok Tedi and the Fly River and all of its tributaries," he said.
"Everybody wants that mine to be shut. Enough is enough. We have suffered enough."
BHP divested its majority share of the mine to the PNG Sustainable Development Program in 2001 and was granted legal immunity in return.
The PNG government seized 100% ownership of Ok Tedi Mine last year and repealed laws that would allow people to sue mining giant BHP Billiton over environmental damage.
But while the move apparently clears the path for people to take legal action against the company, BHP said it was confident it had indemnities in place to protect shareholders from potential claims.
The case will be called to court on February 12.