Kenyan security forces have carried out 25 extrajudicial killing in the last two years in a crackdown on militants, Kenya's official rights body says.
The Kenya National Commission on Human Rights said it had also recorded 81 "enforced disappearances" since 2013.
The report covers the period since the attack on Westgate shopping centre in Nairobi by Islamist militants.
It added that it was concerned that ethnic Somalis and Muslims were being disproportionately targeted.
There has so far been no official response to the report by the government-funded agency.
The al-Shabab Islamist group, which is based in neighbouring Somalia, has been increasingly operating in Kenya.
It was behind the four-day siege on the Westgate mall in the capital that killed 67 people in 2013 and the raid on Garissa University in which 148 people died in April this year.
The Kenya National Commission on Human Rights (KNCHR) said combating terrorism through "official terror" was counter-productive.
In the report, The error of fighting terror with terror, the KNCHR said it had recorded 120 "egregious" violations by the security agencies.
"These violations are widespread, systematic and well co-ordinated and include but are not limited to arbitrary arrests, extortion, illegal detention, torture, killings and disappearances," the report says.
It said it had testimonies of suspects being rounded up and detained for periods "ranging from a few hours to many days in extremely overcrowded and inhumane and degrading conditions".
The report also confirmed the existence of "suspicious graves" in Wajir county and Lanbib in north-eastern Kenya "containing remains of dead persons whose circumstances of death remain unexplained".
The commission's staff had also received threats while trying monitoring the alleged violations, it said.
Human rights violations by the security forces "only served to foment further resentment, increase radicalisation and fertilises the breeding grounds of future terrorists," the KNCHR said.
It called on the president to condemn the abuses, apologise to the victims and for investigations to begin so that those responsible were prosecuted.
BBC Africa's security correspondent Tomi Oladipo says Kenyan security forces have faced similar criticisms from other human rights groups after crackdowns on predominantly Muslim communities in the aftermath of the Westgate and Garissa attacks.