The New York-based rights group, in a new report released Wednesday, said the migrants had faced abuses, including "torture, rape and killings in squalid detention centers" before setting off on their perilous journey, AP reported.
It said some had been detained after being intercepted by the Libyan Coast Guards at sea.
The HRW report is based on interviews conducted with refugees in June on the Italian island of Sicily.
Last month, the EU expanded its anti-smuggling operation in the central Mediterranean to include training Libyan coastal and naval forces, which are intercepting boats and returning migrants to Libya.