More than 869 women were killed in the name of honour while 56 were killed for giving birth to a girl child last year.
Around 687 people were killed in more than 200 sectarian attacks last year, a rise of 22 per cent from 2012, which saw one the deadliest attacks against Christians that claimed lives of at least 100 people in Peshawar Church.
Pakistan's small Christian, Hindu, Ahmadi and Sikh communities face discrimination and sporadic violence.
Violence against shiite Muslims, who make up about 20 per cent of the population, has seen an upward swing in recent years.
The independent Human Rights Commission of Pakistan (HRCP) said most serious violation were committed against women as another 800 committed suicide.
The group criticised authorities for their failure to improve the human rights situation in the country and protect the rights of minorities.
HRCP, in its 'Sate of Human Right 2013 report' launched here, noted serious violation of basic rights of people, ranging from attack at minorities to killing of media practitioners and imprisonment of Indian fishermen.
The report also noted the extra-judicial killing by police, saying that 503 people were killed and 49 injured in 357 police encounters in the country.
In the on-going ethnic and sectarian violence in Pakistan's mega Karachi city in the south, 3218 people were killed, 14 per cent up from 2012.
HRCP secretary general I A Rehman said that government failed to uphold the basic rights of the people and formulate a plan to stop their violations.
He also expressed concern over the attack on journalist Hamid Mir, who survived the attempt on his life in Karachi.
"We are extremely concerned over this and we feel that journalists are at risk in Pakistan and they are not being protected. We are also extremely concerned over lack of unity."
HRCP also said that the 31 US drone attacks in the tribal region in the northwest killed 199 people.
The report, however, praised the completion of the tenure of the elected government, saying it was a significant development for a democratic polity in Pakistan.
