The Human Rights Commission of Pakistan's annual State of Human Rights report said over 100 Shia Hazaras were killed in Balochistan province alone during 2012.
At least 2,284 people died in ethnic, sectarian and political violence in Pakistan's largest city of Karachi during the period.
A total of 87 people were listed as "missing" or detained without charge by security agencies. Of them, 72 people were subsequently traced or released by authorities, the report said.
The report also noted that there had been a decrease in US drone attacks on Pakistan's restive tribal areas, with the number of missile strikes falling from 74 in 2011 to 48 in 2012.
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"Estimates of casualties varied between 240 and 400," the report said.
Referring to major terrorist attacks, the report said hundreds of militants blew up the gates of a central prison in Bannu in March last year and succeeded in releasing 384 prisoners.
In Karachi, at least six churches were attacked, two of them within a period of 10 days in October, it said.
The report also highlighted the condition of jails across the country.
There were a total of 75,444 prisoners in jails across the country, as against the authorised capacity of only about 44,600.
There were 1,289 juvenile prisoners in jails and an overwhelming majority of them was under trial.
Fifty-nine prisoners died in custody while another 81 were injured. Ten incidents of alleged torture of prisoners were reported.