Its youth wing was responsible for attacking and killing opposition supporters, the rights group said.
The CNDD-FDD party has not has yet commented on the allegation.
Burundi is recovering from a brutal civil war that ended with President Pierre Nkurunziza's election in 2005.
Speculation is rife that he intends to run for a third term in the June 2015 election, despite opposition claims that this would be in violation of the constitution which imposes a two-term limit.
The CNDD-FDD's youth wing, Imbonerakure, has "strong links to the security  services and are responsible for perpetrating human rights abuses with  impunity", Amnesty said in a report.
At least one opposition member was shot and killed by two soldiers on the orders of a local official and an Imbonerakure member, Amnesty said.
"Another opposition member had his teeth knocked out during a beating," the report said.
Burundi's ruling party is waging a "relentless campaign of intimidation" against its critics ahead of presidential elections next year, Amnesty International says.