In its report, published this week, Amnesty documented in detail atrocities it said had been committed by the Arakan Rohingya Salvation Army (ARSA) near a remote village in Rakhine State.
The report, citing witnesses, including Hindu women who said they were abducted by ARSA insurgents, said fighters from the group killed as many as 99 Hindus near Kha Maung Seik after launching the raids on security posts on August 25.
"We categorically deny all of these unjustifiable and careless serious criminal accusations mentioned in the said report," ARSA said in a statement signed by its leader Ata Ullah and posted on social media network Twitter late on Friday.
Myanmar has rejected the accusations of ethnic cleansing, as well as most of the accounts of killings and rape recounted by many of the refugees arriving in Bangladesh.
Tirana Hassan, Amnesty International's Crisis Response Director, said the group "absolutely stands by the findings" of its investigation and urged Myanmar authorities to allow unfettered access to northern Rakhine for UN and other independent investigators.