Zaki, 40, had been publicly critical of extremist cleric Abdul Aziz and militant sectarian groups.
On May 7, four unidentified gunmen opened fire on Zaki at a restaurant in Karachi, killing him and wounding two others.
Zaki had been receiving threats and had confided to friends that he was on several militant “hitlists”.
“A thorough and impartial investigation with proper witness protections is absolutely critical to ensure those responsible for Khurram Zaki’s death are brought to justice,” said Human Rights Watch.
“It’s appalling that activists who are at the forefront of opposing violence by militant groups should themselves become targets.”
The Hakeemullah group, a relatively unknown faction of the Pakistani Taliban, claimed responsibility for the murder in a phone call to Reuters, saying Zaki was targeted because of his stance against Abdul Aziz.
On May 9, the police registered a criminal case against Abdul Aziz, Arungzeb Farooqi, a leader of the anti-Shia Ahle-Sunnt-Wal-Jammat (ASWJ), and unidentified gunmen.
Abdul Aziz has been acquitted in several criminal cases in the past because witnesses recanted their statements.
Similarly, the Pakistan government has failed to hold ASWJ and its affiliate, the militant Lashkar-e-Jhangvi (LeJ), accountable for attacks on people from the Shia Muslim community.