The army had earlier on Friday posted a video clip of Trump's directive to his country's military where he said they should consider stones thrown at them by asylum-seeking migrants as rifles.
The Nigerian army quickly seized on Trump's comments, posting a video of Trump's speech on Twitter and telling viewers to draw deductions.
"They want to throw rocks at our military, our military fights back", Trump said in his November 1 remarks.
"I told them (troops) consider it (a rock) a rifle". As for the troops faced with rock-throwers, "they don't have to fire", he added.
Amnesty International estimates that 45 peaceful demonstrators were killed during that melee, while the Nigerian army insists that only six armed protesters were killed.
The U.S. Embassy and Consulate in Nigeria issued a statement Thursday expressing concern about the "deaths resulting from clashes between Nigerian security forces and members of the Islamic Movement of Nigeria".
The IMN leader, Ibrahim Zakzaky, has been in custody since 2015, when an army crackdown allegedly killed 300 of his supporters who were buried in mass graves, according to rights groups.
The police arrested 400 IMN members on Tuesday for engaging in a violent protest and for setting ablaze a police patrol auto parked in front of a shopping mall on Adetokunbo Ademola Crescent, Wuse II, Abuja.
"Video footage and eyewitness testimonies consistently show that the Nigerian military dispersed peaceful gatherings by firing live ammunition without warning, in clear violation of Nigerian and global law", Osai Ojigho, executive director of Amnesty worldwide Nigeria, said in a statement Wednesday.
Samantha Power, who served as ambassador to the United Nations under President Barack Obama, tweeted an image of the now-deleted Twitter post by the Nigerian military.
When a reporter asked him about this, the president said the USA military should "consider it a rifle". The human rights group said the protesters were killed by security forces using automatic weapons on Saturday and Monday in Abuja, the capital, and the neighboring state of Nasarawa.
The army did not mention the fact that the U.S. embassy in Abuja has urged Nigerian authorities to "take appropriate action to hold accountable those responsible for violations of Nigerian law".
Zakzaky was arrested in the aftermath of an alleged attempt to kill Nigerian Army Gen. Tukur Buratai in December 2015. "So, a stone is a weapon", he said.
"Video footage and eyewitness testimonies consistently show that the Nigerian military dispersed peaceful gatherings by firing live ammunition without warning, in clear violation of Nigerian and global law", an Amnesty statement read.