While there have already been several flashpoints between the two title hopefuls, Boullier believes it is inevitable team personnel will also become polarised in their support of one driver - a dynamic he says is exacerbated by the Silver Arrows' current dominance.
"It is an impossible task," he told a McLaren Mercedes phone-in when asked about the difficulties Mercedes face in keeping everyone in the team happy over the remaining 2014 races.
"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 them [Hamilton and Rosberg], and obviously it is very difficult to keep the team in harmony because everyone has their own favourite, which is a human feeling."
Boullier, who managed Kimi Raikkonen in his role as team principal at Lotus before joining McLaren, added: "I am not in this situation so far, so it is okay so far for me."
McLaren are locked in a fight with Force India for fifth place in the 2014 constructors' championship. With Jenson Button retiring and Kevin Magnussen finishing 10th at the last round in Singapore, McLaren currently trail their rivals by six points, 111 to 117.