The Human Rights Commission of Pakistan's report said 418 Muslims of various sects were killed in terror attacks and about 25 per cent of Sikh families in the Orakzai tribal area were forced to leave their homes due to threats from Taliban.
It said 500 Hindu families from Balochistan province migrated to India due to threats to their lives and security.
The "State of Human Rights in 2010" report, which detailed attacks on the minorities, said: "All indications suggest that there are even worse times ahead." The report said 418 people were killed in violence against different minority Muslim sects while suicide attacks on Muslims injured 628 people, including Shias.
Sikhs living in Pakistan's northwestern areas for centuries had to face trying times after the Tehrik-e-Taliban Pakistan asked them to pay ''jiziya'' (a religious tax) or leave the area.
Around 25 of the 102 Sikh families living in Orakzai Agency were forced to flee their homes. They were able to return after the military carried out an operation against the militants.
A total of 500 Hindu families from Balochistan in southwest Pakistan migrated to India because of threats to their lives and security, the report said.
According to Balochistan's director of the Federal Human Rights Ministry, at least 27 Hindu families from the province had sought asylum in India because of threats, it added.
The minority Ahmedi sect, which was declared non-Muslim through a constitutional amendment in 1974, lost 99 members to faith-based violence, the report said.
The report further said 64 people were charged under the controversial blasphemy law in 2010 and many of them were imprisoned. A Muslim and two Christian men accused of blasphemy were killed in police custody, it said.
Highlighting the abuses of the rights of minority communities, the report said there had been few positive developments with regard to freedom of thought, conscience and religion.
"Extremist views grew more vociferous as voices for basic human rights and tolerance became more isolated in face of violence and intimidation," the report noted.
It said police were not doing enough to protect minorities from attacks and had even been accused of harassing or being complicit in framing false charges against them.
Presenting the report, HRCP chairman Mehdi Hassan claimed most human rights abuses were being conducted by government functionaries, including police.
"Under such conditions, who will ensure that the laws are being implemented?" he asked.
The report said prejudices of law enforcement personnel were believed to be a hurdle in effective protection of religious minorities in serious danger from the Taliban and sectarian militant groups.
HRCP secretary general I A Rehman said in most religion-based killings, the federal and provincial governments failed to even express sympathy with victims.
The report also highlighted the growing spread of hate literature and said even mainstream Urdu newspapers featured 1,468 news articles and editorials that promoted hate, intolerance and discrimination against Ahmedis.
Rehman contended that political parties had failed to contribute towards improving human rights conditions.
"They cannot even speak clearly on the issue because they are not true political parties, these are just brokers and rubber-stamps," he alleged.
The report further highlighted the government's weak response to misuse of the controversial blasphemy law and its flip-flop on calls to reform the law to prevent its misuse.
Observers have said that the PPP-led government had apparently shelved plans to review the law following the assassination this year of Punjab Governor Salmaan Taseer and Minority Affairs Minister Shahbaz Bhatti, who were gunned down for challenging the law.
The report also detailed the law and order situation, saying about 12,580 people were murdered and 581 kidnapped for ransom in 2010. A total of 16,977 cases of kidnapping were reported.
The HRCP held US drones strikes responsible for 957 extra-legal killings and said another 338 people were killed in police "encounters" or fake shootouts.
A total of 1,159 people, included 1,041 civilians, were killed in 67 suicide attacks, the report said. Overall, a total of 2,542 people were killed and 5,062 injured in terrorist attacks.
Target killings in Karachi claimed the lives of 237 political activists and 301 civilians, the report said.
Another 118 people were killed and 40 injured in 117 incidents of target killing in Balochistan. The figures included 29 non-Baloch settlers and 17 members of the Shia Hazara community.
The bodies of 59 "missing persons" people detained without charge by security and intelligence agencies were found in Balochistan.
The report said there were 163 attacks on educational institutions while militants killed 22 teachers in Balochistan between January 2008 and October 2010.
A total of 791 women were killed in the name of honour while 2,903 were sexually assaulted, with the maximum number of cases reported from Punjab province.