The rights organization said Monday no one was arrested following June clashes in Benghazi that left 32 people dead. Little has been done for justice in November clashes in Tripoli that left at least 46 people dead.
"It's bad enough the authorities seem to be powerless to defend Libyan citizens, but they need to make greater efforts to investigate the deaths of dozens of people," Sarah Leah Whitson, Middle East and North Africa director at Human Rights Watch, said in a statement Monday.
Libyan Prime Minister Ali Zeidan said his country has made strides since civil war ended in 2011.
"The Libyan people have had a long struggle, and lately they have done a lot to get rid of the militias," he said in a statement alongside British Foreign Secretary William Hague last month in London.
Whitson, however, said militias are operating in Libya with "de-facto immunity," escaping prosecution routinely during the two years since civil war ended.
"Libya's future stability is at risk unless there is a concerted effort by the Libyan authorities to change that and start indicting wrongdoers," she said.
Protests against Libyan leader Moammar Gadhafi erupted in Benghazi in 2011, pushing the country into civil war.