The Kathmandu-based human rights' group Informal Sector Service Centre in a report claims people have suffered either physically or economically in the violence that has swept the impoverished country since 1996.
Many of Nepal's 24 million people have also known someone killed or wounded in the conflict.
The group said 18,000 Nepalese were currently displaced and that since 1996, about 400 people have "disappeared," including a number of non-Maoist local leaders abducted by the rebels.
But the group's president, Subodh Pyakurel, has accused the government forces of turning to abductions as well.
"People have begun to disappear at the hands of the royal army just as has happened at the hands of the Maoists," he said.
The startling disclosures come amid an upsurge of violence in the kingdom, following the collapse of a ceasefire between the government and the rebels in August.
The rights' group said 1213 people had died in fighting since the ceasefire ended.
The Maoists have been battling government forces, seeking to change the country's constitutional monarchy with a communist republic.
The conflict has killed more than 8000 people since it started.