The human rights organization lists torture, extrajudicial executions and detention without trial among the abuses committed by security forces.
“The cycle of attack and counter-attack has been marked by unlawful violence on both sides, with devastating consequences for the human rights of those trapped in the middle,” said Salil Shetty, Secretary General of Amnesty International, in a statement.
“People are living in a climate of fear and insecurity, vulnerable to attack from Boko Haram and facing human rights violations at the hands of the very state security forces which should be protecting them.”
The Amnesty report claims that many innocent civilians have been targeted by security forces and that their heavy-handed tactics only do more to radicalize potential terrorists.
“Every injustice carried out in the name of security only fuels more terrorism, creating a vicious circle of murder and destruction,” said Shetty.
The Nigerian government has responded to the report, denying that security forces have committed any abuses.
"I think you need to look at the circumstances,” Nigeria's Finance Minister Ngozi Okonjo-Iweala told the BBC.
“When the UK was battling terrorism... the US, they had Guantanamo Bay.... all countries, when the security of their citizens is at stake, they try to use all the tools at their disposal."