Pakistani journalists and activists faced an increasingly hostile climate in 2015 due to harassment, threats and violence from both security forces and militant groups, Human Rights Watch said on Wednesday.
In its 659-page World Report 2016, it said the government, under pressure from the military, placed new restrictions on the funding of civil society groups.
"Pakistan should reverse course and repeal or amend laws curbing freedom of expression and association," said Brad Adams, Asia director at Human Rights Watch.
"The government should never use the threat of extremist violence as a pretext to violate the rights of independent voices."
The Taliban and other armed groups threatened media outlets and targeted journalists and activists for their work, the report said.
However, the Pakistani media was deterred from reporting on or criticizing human rights violations by the military in counterterrorism operations.
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In December 2014, the Islamist Tehreek-e-Taliban, the Pakistani Taliban, attacked a school in Peshawar, leaving 148 dead, almost all of them children.
The government responded with a national action plan to fight terrorism, including tactics that violated basic rights, the rights body said.
Abuses by security forces, particularly following the Peshawar attack, led to thousands of Afghans living in Pakistan to return to Afghanistan or flee elsewhere.
Religious minorities faced violent attacks, insecurity and persecution - largely from Sunni extremist groups - which the government failed to address, Human Rights Watch said.
The government continued to use blasphemy laws to institutionalize discrimination against religious minorities, it said.