While no-one has been charged, Bruyneel was among five people, including Armstrong, who were notified by the USADA of the allegations against them.
USADA said they had forwarded their allegations to the Anti-Doping Review Board, which would decide whether to proceed with the case.
Bruyneel was accused of conspiring in an orchestrated doping programme between 1998 and 2011.
Although USADA said they had no analytical proof, they said they had taken statements from former team members, who they have not identified.
"I am dismayed that once again doping allegations have been raised against me, this time by USADA," Bruyneel said in a statement.
"Following a Department of Justice Grand Jury investigation, no charges were filed against me.
"It cannot be right that I or anyone else can be pursued from court to court simply because our accusers do not like the decisions made along the way and so attempt to find a court which will get them the result they want."
Bruyneel served as Armstrong's team manager when the American cyclist, a cancer survivor, won the Tour de France a record seven times.
Although he never failed a doping test and always denied accusations of wrongdoing, Armstrong has been dogged for years by claims he cheated.
The US Justice Department spent two years investigating similar claims against him but closed their case in February without laying any charges against him.
Earlier in the week, Armstrong also issued a statement dismissing the latest accusations against him.
"I shall of course co-operate fully with the investigation, although I have no doubt the end result will be the same as all the other investigations over the years," Bruyneel said.