Days earlier, Nigerian army soldiers opened fire on protesting members of the Shia Islamic Movement of Nigeria (IMN), some of whom were throwing stones, killing 42 people, according to group leaders.
The army posted a now-deleted tweet featuring a video of Mr Trump encouraging armed troops to shoot at any Central American refugees and migrants who throw rocks at authorities when crossing the U.S. border.
The army's official Twitter account posted a video, "Please Watch and Make Your Deductions", showing Mr. Trump's speech on Thursday in which he said rocks would be considered firearms if thrown toward the American military at the nation's borders. "We're going to consider it, I told them, consider it a rifle". "They want to throw rocks at our military, our military fights back", said Trump.
One day later, Trump said he didn't mean the troops would shoot the rock-throwers. "I told them, consider it a rifle".
The tweet comes just days after the army shot and killed 45 Muslim protesters in the capital city of Abuja.More news: Facebook Private Message Hack: Are We Going to Be Affected?
"We urge Government of Nigeria authorities to conduct a thorough investigation of the events and to take appropriate action to hold accountable those responsible for violations of Nigerian law", the embassy said.
At least 45 supporters of the Islamic Movement in Nigeria were killed by security forces on Saturday and Monday, as the group held two days of "peaceful gatherings" around Abuja, according to the London-based worldwide human rights watchdog.
The Islamic Movement of Nigeria (IMN) claimed 49 of its members were killed after the army and police fired live bullets at crowds who marched near and in the capital, Abuja. IMN represents many members of Nigeria's Shiite minority and opposes the use of violence.
The Nigerian military has said as many as six soldiers were wounded during the protest after "thousands" of members of the sect overran a police checkpoint and blocked traffic along a highway.
"In Abuja, Nigerian Army killed 46 of our members, injured 110 others but they are denying that only three persons were killed. But they do that with us, they're going to be arrested for a long time".More news: Marcus Rashford helps Manchester United make 2-1 comeback against Bournemouth
Asked about the president's remarks, a Pentagon spokesperson said, "We will not discuss hypothetical situations or specific measures within our rules on the use of force, but our forces Are trained professionals who always have the inherent right of defense".
The military did not return calls seeking comment on the deleted tweet.
Nigerian Army spokesman Brigadier General Texas Chukwu did not respond to ABC News' requests Friday for comment on the tweet and why it was taken down.
The Nigerian government came under harsh criticism after Amnesty International reported the killing of Shiite Muslim protesters by Nigerian security forces.
Amnesty's Nigeria Executive Director, Osai Ojigho, on Saturday in a statement said the basic rights of humans are not subject to the whims and caprices of leaders.More news: Critics compare Trump's midterm spot to racist Willie Horton ad from 1988
Speaking to LEADERSHIP Sunday in Sokoto, state leader of IMN, Sheikh Sidi Manir, said they have been practicing their religion in Nigeria for over 40 years now without interference, hence, he wondered what is now their crime that the government is consistently against them.