"Johan's name is cited 129 times in the report," Cancellara was quoted as saying by the Belgian newspaper Het Laatste Nieuws on Friday.
"I don't know if I can still work with Johan. We'll see what happens next. I want to know what happened."
Cancellara, who is also the 2008 time trial Olympic champion and a double Paris-Roubaix winner, joined RadioShack-Nissan this season after his Leopard Trek team merged with the American outfit.
The Swiss had never worked with Bruyneel before.
Bruyneel was Armstrong's team manager in all of his seven victorious rides on the Tour de France and is described in the USADA report as a key element in an organised doping ring.