Nigeria is "concerned" about Amnesty International's activities, a spokesperson for President Muhammadu Buhari said on Monday, just days after the government briefly banned Unicef over claims it was training "spies" sympathetic to Boko Haram.
"The federal government is increasingly concerned about the role that Amnesty International is playing in the war against terror in Nigeria," Garba Shehu said in a statement.
"The organisation's operations in Nigeria seem geared towards damaging the morale of the Nigerian military," he said.
"It often appears as if the Nigerian government is fighting two wars on terror: against Boko Haram and against Amnesty International."
The statement comes on the same day that the Nigerian military threatened the "closure" of the global rights watchdog in a statement posted on Facebook.
Army public relations director Brigadier General Sani Usman said Amnesty was "determined to destabilise" Nigeria through the "fabrication of fictitious allegations of alleged human rights abuses" and "clandestine sponsorship of dissident groups to protest".
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The military has in the past been critical of international organisations operating in the country and has hit out at organisations reporting that it committed rights violations and war crimes during its fight against Boko Haram.
The bloody Islamist uprising in northeastern Nigeria began in 2009 and has spread to neighbouring Cameroon, Chad and Niger, killing at least 27 000 people and leaving millions dependent on aid for survival.
On Friday the military banned Unicef from operating in the country over claims it was training "spies" who support Boko Haram.
It retracted the ban within hours following an "intervention by well meaning and concerned Nigerians," according to an army spokesman.
President Buhari, who came to power in 2015 pledging to end the violence, is under increasing pressure to act as he gears up to seek re-election in a February ballot.
The 76-year-old former army general has come under attack for previously claiming the jihadists were "technically defeated".