"We didn't sign up for a deal in which this type of corruption would enter the program," BP attorney Jeff Clark told Barbier before he ruled.
Plaintiffs' attorneys say the company hasn't provided any evidence that Juneau has improperly paid any claims.
BP spokesman Geoff Morrell said the company disagreed with Barbier's ruling and would review its legal options.
"There is a material risk that payments going out the door have been and continue to be tainted by possibly fraudulent or corrupt activity, and BP should not be forced to bear the risks of improper payments pending the outcome of Judge Freeh's investigation," Morrell said in a statement.
Clark, the company's attorney, said BP's request to halt payments until after the investigation was relatively modest because in many cases it won't be possible to recoup fraudulent payments.
Stephen Herman, one of the lead plaintiffs' lawyers, said BP agreed to Juneau's appointment and was pleased with his work before a recent dispute over his interpretation of settlement terms governing business claims.
"Now he's become their scapegoat," Herman said.
Rick Stanley, one of Juneau's lawyers, said BP's request to suspend all payments was unnecessary. Juneau's internal probe of the misconduct allegations hasn't turned up any evidence that Sutton or his wife could have manipulated the calculation of claims payments or had any "undue influence" on policy decisions.
"They had some involvement in those policies, but Juneau was ultimately responsible," he said. "That is his final decision."
Barbier has authorized Freeh to conduct an independent investigation of the alleged misconduct and take a broader look at the claims program. The former FBI director hasn't indicated how long it will take to complete his investigation.