Massa, no stranger to unwelcome radio messages at his previous team Ferrari, finished the second race of the Formula One season in seventh place and just ahead of his frustrated Finnish teammate.
McLaren's Jenson Button was sixth, managing to hold off the Williams pair despite struggling for straight line pace.
Williams Chief Operations Engineer Rod Nelson said the team felt Bottas had fresher tires than Button and would have been able to challenge the Briton better than Massa, whose rising engine temperature was causing concern.
The Brazilian didn't see it that way and said he had been surprised to hear the message "Valtteri is faster than you, do not hold him up" over the team radio.
"What I did was correct and I try and do the best for the team. I'm sure the result will not change if I let him by. What I did in my opinion was correct and I'm doing everything I can to help the team," he told reporters.
"The team respect me 100 percent and they showed they respect me after the race so I have no problem at all. What happened today was not what I expect but what I did was correct," added the Brazilian.
"The problem was I was much quicker than McLaren the whole race but going out the last corner they had very good traction… Valtteri had the same problem, overtaking McLaren was not easy."
Nelson said the plan had been for Bottas to attack Button but if he wasn't able to overtake, then Massa would have been allowed to reclaim seventh from the Finn.
Choosing his words carefully, Nelson said there would be a discussion with both drivers later to discuss the matter and that it was "a strategic decision" rather than team orders.
"He didn't do what we would have preferred him to do," he said of Massa.
"We look to maximise our constructor points whenever we go racing, Felipe was running high temperatures on his engine and we were a little bit concerned about it and Valtteri had much fresher tyres, certainly than Jenson did.
"We thought it would be good to give Valtteri a go against Jenson and then if he hadn't achieved that in two or three laps we would have swapped our drivers over again."
Nelson said Williams did not have team orders.
"Its not like other teams where they have a No 1 driver and a No 2 driver, we have two No 1 drivers. And its a race situation," he explained.
"We will go through with the drivers tonight and discuss what we expect."
Bottas was in sombre mood after addressing reporters after Massa, initially trying to steer questions off the subject, which took the shine off Williams moving into fourth on 20 points in the constructors standings.
The Finn said he had followed a subsequent instruction by not overtaking Massa in the final two laps before contradicting the Brazilian's version of discussion in pre-season.
"We have spoken beforehand about these situations but I think we need to go more into the details," the Finn said, adding he believed he could have overtaken Button.
"We are going to talk through it and what do we need to do next time in similar situations so everything is clear. What are the rules… and (hopefully it) allows us to get more points."
The wording of the message would have been particularly painful for Massa, who was famously told "Fernando is faster than you" while leading the 2010 German Grand Prix.
On that occasion, he moved over to let teammate Fernando Alonso win in what he later described as the toughest moment of his career with Ferrari.
Last year's Malaysian Grand Prix had two similar controversies, with Red Bull's world champion Sebastian Vettel ignoring a coded 'multi 21' instruction and passing teammate Mark Webber for victory.
Mercedes' Nico Rosberg, who finished second behind teammate Lewis Hamilton in Sunday's race, obeyed an order last year to hold station behind the Briton. supersport.com