Mr Shehu says he did not blame the farmers, victims of the massacre, for the unfortunate incident.
The dozens of farmers killed by Boko Haram in Zabarmari on Saturday had no permission to be there, presidential spokesperson, Garba Shehu, has said.
Mr Shehu said this in an interview with the BBC Monday morning. He repeated it in a Facebook post while trying to clarify his earlier statement.
He, however, said he did not blame the victims of the massacre for the unfortunate incident.
In an interview on BBC on Monday morning, Mr Shehu had said the farmers "did not get military clearance to be on the rice farms when the attack happened
PREMIUM TIMES reported the Saturday attack on mostly rice farmers in Zabarmari, a community in Jere Local Government Area, with residents saying at least 43 farmers were killed.
President Muhammadu Buhari who condemned the attack in a Saturday night statement did not speak on the casualty figure.
PREMIUM TIMES reported how the victims were buried on Sunday with residents claiming many more are yet to be accounted for.
On Sunday, the UN resident coordinator in Nigeria, Edward Kallon, said the death toll from the attack "could be as high as 110."
Mr Shehu, while explaining the reason for his comment, said there were military procedures in war zones like the North-east, hence his comment on the "military clearance".
"Today, I found myself leading the trends in the social media for the wrong reasons," Mr Shehu said. "The State of Borno is essentially a military zone up till now that we are talking and much of what people do; much of where they go are governed by the exigencies of security."
"Routinely, traders, administration officials and even UN agencies get the green light to go to many of the areas to avoid trouble.
"Information from security agencies says that the Zabarmari marshlands are infested with land mines and movements in around those areas subject to military oversight.
"No one is delighted with the massacre in Zabarmari and there is nothing anybody will gain by playing blame games."
"The question I tried to answer on BBC was: did the security sign off on the area as being free of mines and terrorists? The honest answer is, no," Mr Shehu added.
"I'm human with tons of compassion and empathy, and could not have said that the victims deserved their fate for ignoring security clearance," the official also said.
He said he was "merely explaining the mode of military operations in the war zone of the North-east".
"There are areas that are still volatile that require security clearance which is intended to put people out of harm's way," he said.
He said, "when tragedies occur, questions arise in terms of how something happened in order to avoid future recurrence."
"Informing the military of our movements in an area of volatility and uncertainty is intended to preserve public safety.
"Explaining why something happened doesn't mean I have no sympathy for the victims. I was just explaining the military procedures on the safe movement of the people and not supporting the death of the victims," the former president of the Nigerian Guild of Editors added.