The commander-in-chief said rocks would be considered the same as firearms if thrown at United States troops whom he had deployed to the southern border, warning that the Americans could shoot the migrants if attacked.
The tweet on the Nigerian army's Twitter account stated: "Please Watch and Make Your Deductions". "We're going to consider it, I told them, consider it a rifle". He added: "They want to throw rocks at our military, our military fights back".
But Trump said Saturday that he only meant immigrants throwing rocks would be arrested. "When they throw rocks like what they did to the Mexican military and police I say consider it a rifle".
The tweet was posted just days after clashes between Nigerian soldiers and Shia Muslims once again turned deadly.
"We call on both sides to exercise restraint, and we urge the Government of Nigeria to conduct a thorough investigation & hold accountable those responsible for violating Nigerian law".
The Nigerian army says six protesters have been killed, but the protest group itself says dozens died, and rights group Amnesty International says the true number is 45.
The Islamic Movement in Nigeria (IMN), otherwise known as Shiites, yesterday, vowed to continue their protest in Abuja, Nigeria's capital until their leader, Sheikh Ibrahim Elzazaky, is released unconditionally as directed by the court two years ago.
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".
Trump, however, has made clear his intention to strengthen the US-Nigerian partnership, despite minimal efforts by Nigeria at genuine reform.
During Zakzaky's 2015 arrest, Nigerian soldiers are believed to have killed hundreds more members of the group.
When a reporter asked him about this, the president said the USA military should "consider it a rifle".
Earlier in a statement responding to Trump's remarks, Amnesty International's Secretary General Kumi Naidoo said: "We reject these vicious policies". The IMN said that the military killed at least 49 people with their live bullets.
The Nigerian government came under harsh criticism after Amnesty International reported the killing of Shiite Muslim protesters by Nigerian security forces.
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.
"What did the biblical David use to kill Goliath?"
Nigerian army points to Trump's recent comments on rock-throwers to justify deadly attack on Shia protesters. "Many of these shootings clearly amount to extrajudicial executions", said Osai Ojigho Director of Amnesty International Nigeria in a statement.