A joint statement released by Amnesty International and Human Rights Watch, HRW said, "freedom of expression, dissent, and media freedom are vital for the enjoyment of other rights and holding the government accountable."
The two groups pointed out that since the July coup that toppled President Mohamed Bazoum, the ousted leader has been held in the presidential residence with his wife and son.
Amnesty and HRW said several ministers of the deposed government have been incarcerated in the country.
"Amnesty International and Human Rights Watch consider their detentions as arbitrary for being politically motivated," read the joint statement.
Local and international journalists in Niger "have been threatened, verbally harassed online, and physically attacked," the statement added.
The two NGOs highlighted as an example the case of Niger journalist Samira Sabou, who was charged last month with "production and dissemination of data likely to disturb public order" before being released on bail almost two weeks later.
The Niger operations of French broadcasters Radio France Internationale, RFI, and France 24 have been suspended by the military authorities since early August.
Speaking to HRW, a Nigerien journalist said, "self-censorship has become a survival tactic for many of us."
Ilaria Allegrozzi, a senior Sahel researcher at HRW, said Niger's governing junta should "end arbitrary detentions, uphold human rights, and allow media freedom."
Ousmane Diallo, a Sahel researcher at Amnesty International's regional office for West and Central Africa, supported Allegrozzi's statement.
"Niger is at a critical juncture," Diallo said.
Amnesty and HRW said supporters of Niger's new rulers have been committing physical violence in the streets of Niamey.
West Africa's regional ECOWAS bloc has warned military intervention should diplomatic efforts to return Bazoum to power fail.