Officials found the male rhino with its horn gouged out in Chitwan National Park, the country’s biggest rhino conservation area.
“We performed a post-mortem and found that it had been hit by a bullet on its head,” the park’s spokesman Nurendra Aryal said.
Aryal said a team had been set up to investigate the incident and security had been tightened at the district borders.
In September last year a rhino died weeks after poachers shot it in the same park, the first of the rare animals to be killed in the country in over two years.
Thousands of one-horned rhinos once roamed the plains of Nepal, but their numbers have plunged over the past century due to poaching and human encroachment on their habitat.
The population decline was particularly dramatic during Nepal’s 1996-2006 civil war, when soldiers on anti-poaching duties were redeployed to fight the Maoist guerrilla insurgency.
But the country has since made rapid progress in combating the poachers who kill the animals for their prized horns, drawing praise from conservation groups and activists.
The horns fetch huge prices in some Asian countries where they are used for medicines and jewellery.
Nepal is home to about 645 rhinos, out of which about 600 live in Chitwan National Park.
The park is in the process of relocating five rhinos to another conservation area in far-west Nepal to boost their population.
Shant Raj Jnawali, a rhino expert at WWF, said the latest death highlighted the vulnerability of the animals despite anti-poaching efforts from the community, park wardens and army.
“We hope that the investigation will help us devise new strategies to strengthen protection for these animals,” Jnawali said.
Rhino poaching carries a maximum penalty of 15 years in jail and a 100,000-rupee (B34,660) fine.