The Nicaraguan Association for Human Rights (ANPDH) says it has closed its offices in the Central American country after its staff received "alarming information" about threats to them.
The group has been denouncing alleged rights abuses by the Nicaraguan government during more than three months of anti-government protests.
It says 448 people have been killed since the protests began on 18 April.
ANPDH said it had information about plans to persecute its staff.
'Threats and harassment'
The group said its workers had received death threats over the phone. The NGO also said that it had learned of plans to accuse staff of fabricated crimes.
ANPDH said the closure of its Managua offices would be "temporary" in order to safeguard the safety of its workers, who had been harassed by armed groups.
Its executive secretary, Álvaro Leiva, and other members of staff have left the country. In a statement, the group said it would continue to receive reports of human rights abuses via email and WhatsApp.
Human rights activists are not the only ones who have reported being harassed and threatened.
Dozens of doctors and health workers have been sacked. They say their dismissals came after they treated injured anti-government protesters.
One of the doctors who was sacked, Javier Pastora, told Spain's El País newspaper that he was told he had been dismissed "for political reasons".
Professors teaching at state-run universities have also reported receiving dismissal letters which they say were issued because of their criticism of the government.
Catholic clergy, who have been mediating in the crisis, have also come under attack from pro-government groups.
ANPDH said its staff had been harassed even before the current wave of protests began but that the threats had become more menacing.
The group has been criticised by the government, which accuses it of inflating the number of people killed and of failing to properly verify reports of alleged human rights abuses.
"They just invent anything. Some of the 'dead' have appeared alive, some of them in the US," President Daniel Ortega told CNN (in Spanish) without offering any evidence of such cases.
President Ortega also accused human rights groups in Nicaragua of being "politicised" and of actively opposing the government.
The number of people killed in Nicaragua since anti-government protests started on 18 April is hotly debated.
In an interview with Euronews broadcast on 30 July, President Ortega said 195 people had been killed.
The Inter-American Commission on Human Rights put the number at 317 as of 30 July, while ANPDH put it at 448 as of 26 July.
ANPDH also says it estimates that 600 people have disappeared since the start of the protests.