Relations between Nico Rosberg and Lewis Hamilton have been fraught as both racers dominate the running for the F1 drivers' title and Boullier has suggested that Silver Arrows' chief Toto Wolff faces "an impossible task" to appease his stars.
He told a McLaren phone-in: "When you are in the position of Mercedes, both drivers can win the championship - and that grows more true race by race.
"There is only one winner - and one loser. Nobody wants to be the loser, and this is why it is impossible to get this harmony within the team.
"To keep people happy is also very complicated. There is clearly a very strong fight between and obviously it is very difficult to keep the team in harmony because everyone has their own favourite, which is a human feeling."
Hamilton leads the drivers' standings by three points from Rosberg after the Briton's victory in Singapore last weekend.
The Mercedes pair resume their battle for the championship at next weekend's Japanese Grand Prix.