"How could we do what to Felipe?" deputy boss Claire Williams responded to a question from British television Sky after the Malaysian grand prix.
At Sepang, Brazilian Massa at least twice ignored radio calls to let his teammate Valtteri Bottas pass him for seventh place.
One of the calls - "Valtteri is faster than you" - was almost eerily identical to Ferrari's infamous 'Fernando (Alonso) is faster than you' of Hockenheim 2010.
But Claire Williams initially tried to deny it was actually an order.
"At the end of the day, Felipe finished ahead of Valtteri," she insisted. "They were both told to cool it."
Asked if the team would be rebuking Massa, Williams added: "I'm going home now. That's me done for the day."
It was chief engineer Rod Nelson who had to acknowledge that Massa "didn't do what we would have preferred him to do" as Grove based Williams pursued the sixth-placed Jenson Button's extra points.
"The facts are we felt that Valtteri stood quite a good chance of getting past Button because his tyres were about five laps younger," Nelson said at Sepang.
He explained that the radio calls were not made because Massa is once again being shuffled into an old Ferrari-like 'number 2' role.
"There's nothing else going on in the background," Nelson insisted. "We don't run like that -- it's not like other teams where they have a number 1 driver and a number 2 driver. We've got two number one drivers."
He said the idea was simply to give Bottas "a go" at passing Button, and if he failed to do it, "we would have swapped our drivers over again".
"We will go through it with the drivers and discuss what we expect," said Nelson.
Toni Vilander, a Finnish racing driver and pundit for MTV3 television, said he thinks Massa should have obeyed the order.
"When a team asks, the driver should invariably follow," he said.
"I think Massa should perhaps have swallowed his pride and let Valtteri through," he added.