Four people were killed in a blast at an Internally Displaced Persons’ camp in Borno State, Doctors Without Borders said on Tuesday.
A Nigerian military source confirmed the incident and put the death toll at five.
The explosion happened at about 12:30 pm on Monday in the border town of Pulka, in the Gwoza area of Borno, where a Spanish team from the medical charity is providing healthcare.
It was initially thought the blast was caused by a suicide bomber.
But a military source in the town said later that examination of the blast scene indicated it may have been caused by a mortar shell.
Ivan Munoz, an MSF spokesman in Borno state, told AFP in an email that the blast killed three people and injured seven, one of whom subsequently died after being admitted for treatment.
“All our staff are safe. The team is monitoring the security situation to assess any further steps,” he added.
The military source, who asked not to be identified because he was not authorised to speak to the media, gave a higher death toll of five.
“We are still examining the fragments (of the mortar shell) to determine where it came from and who is responsible,” he added.
“It is not clear if it was a stray projectile or deliberate attack.”
Boko Haram has carried out attacks before against internally displaced people (IDPs) but using rocket-propelled grenades (RPGs) rather than mortars.
In September last year, at least seven people were killed when the jihadists fired an RPG at a camp at Ngala, also in Borno state near the border with Cameroon.
The camp was set up in January 2016 and housed some 80,000 people, many of them Nigerian refugees who had fled across the border because of the fighting.
IDPs have been particularly vulnerable to attack during the conflict, especially from suicide bombers, exacerbating already difficult conditions for aid agencies working to stave off a humanitarian crisis.
In April, Islamist militants abducted 18 girls and women from Pulka, which is about 110 kilometres (70 miles) southeast by road from the Borno state capital, Maiduguri.
Boko Haram fighters still operate in hard-to-reach rural areas, including the mountains around Gwoza, where in August 2014, Boko Haram factional leader Abubakar Shekau declared a self-styled caliphate.
In Pulka in November last year, troops rescued one of the 216 schoolgirls who were kidnapped from their school in the Borno town of Chibok in April 2014.
MSF provides primary and secondary healthcare in Pulka, including outpatient care, emergency medicine and maternity services, as well as public health projects.