Islamabad: The Pakistan government has failed to act against abuses by security and intelligence agencies, which allowed extremists to attack religious minorities, Human Rights Watch said on Friday.
In its 665-page World Report 2013, it also criticised the authorities for doing little to address attacks against journalists and human rights defenders, and for serious abuses in counter-terrorism operations.
"Pakistan`s human rights crisis worsened markedly in 2012 with religious minorities bearing the brunt of killings and repression," said Ali Dayan Hasan, Pakistan director at Human Rights Watch.
"While the military continued to perpetrate abuses with impunity in Balochistan and beyond, Sunni extremists killed hundreds of Shia Muslims and the Taliban attacked schools, students, and teachers."
Human Rights Watch documented a sharp escalation in persecution of religious minorities in 2012.
At least eight journalists were killed in Pakistan last year. No one was held accountable in any case.
Media coverage of alleged abuses by security forces and militants was impeded by a climate of fear, Human Rights Watch said.
Journalists rarely reported on rights abuses by the military in counter-terrorism operations, and the Taliban and other armed groups regularly threatened media outlets over their coverage.
Human Rights Watch recorded continued enforced disappearances and killings of suspected Baloch nationalists and militants by the military and allied agencies.
Baloch nationalists and other militant groups also stepped up attacks on non-Baloch civilians.
In 2012, well over 400 members Shia Muslims were killed in targeted attacks across Pakistan. In Balochistan, over 125 were killed, mostly from the Hazara community.
The government was unable or unwilling to break the links between Pakistan`s military and intelligence agencies with extremist groups.
Sunni militant groups, including those with known links to the Pakistani military, intelligence agencies and affiliated paramilitaries, such as the ostensibly banned Lashkar-e Jhangvi, operated openly across Pakistan.
The government took no significant action to protect those under threat or to hold extremists accountable.
Suicide bombings, armed attacks and killings by the Taliban, al Qaeda and their affiliates continued in 2012, targeting politicians, journalists, religious minorities and security personnel.
Militant Islamist groups attacked more than 100 schools in 2012, including students, teachers and rights advocates.
The Taliban`s nearly fatal attack on Malala Yousafzai, a 15-year-old girl who was an outspoken advocate for children`s right to education, garnered condemnation from across the world and the political spectrum in Pakistan.
The deadly attacks on minority groups show no sign of letting up in 2013, Human Rights Watch said.
Said Hasan: "The government needs to show some backbone and act urgently to protect vulnerable communities such as the Hazara, or risk appearing indifferent or even complicit in the mass killing of its own citizens."
Human Rights Watch urged Pakistani authorities to promptly apprehend and prosecute those responsible for attacks on Shias and others at risk.
The government should also actively investigate allegations of collusion between Sunni militant, military intelligence and paramilitary forces, and hold accountable personnel found to be involved in criminal acts.
At least 16 people remained on death row and 20 were serving life sentences for blasphemy. Members of the Ahmadi community were major targets.
Security forces routinely violated basic rights in the course of counter-terrorism operations.
Thousands of alleged Taliban members, rounded up in 2009 in Swat and the Federally Administered Tribal Areas (FATA), remained in military detention without charge or trial.