In its annual report, the HRCP said 913 girls and women, including 99 minors, were killed in 2012.
The report said 604 were killed after being accused of having illicit relations with men.
Around 191 were reported slain for marrying their own choice of husbands and going against their families' wishes.
Zohra Yusuf, chairwoman of the HRCP, speaking in a telephone interview with RFE/RL's Radio Mashaal, said many of the perpetrators were close relatives of the victims.
"In most cases they are identified because they happen to be family members," Yusuf said. "They are either the husbands or the fathers or the brothers. ...In some cases they are also arrested. But...in many cases they are allowed to escape. [And] the conviction [rate] is very low."
Honor killings are illegal in Pakistan, but Yusuf said such killings are still carried out in remote tribal areas.
She said many cases of honor killings are the result of decisions taken by tribal courts.
"This is like any murder," she said. "Honor killings should be considered a crime against the state. It is not a case between two parties. It should be considered as murder, which it is under the law, and the system of tribal justice for taking the law into their own hands needs to be addressed."
The independent commission noted honor killings were not restricted to the Muslim community.
It said around seven Hindu and six Christian women were also killed.
Yusuf said the number of honor killings in Pakistan usually ranges between 600 and 900 each year.
The HRCP painted a grim picture of human rights in Pakistan, saying ethnic, sectarian, and politically linked violence in 2012 killed some 8,000 people.