"The recent spike in attacks by insurgents triggered the increase," the IOM said, referring to stepped up attacks by the hardline Islamist group in recent months.
More than 1,000 people have died in Boko Haram attacks since May 29 when President Muhammadu Buhari came to power.
The IMO said the new figure released in Abuja covered internally displaced people (IDPs) in the northeastern states of Adamawa, Bauchi, Borno, Gombe, Taraba and Yobe as well as the central state of Nassarawa and Abuja.
"The increase...can be attributed to the intensification of attacks carried out by the insurgents, as well as to improved access to previously inaccessible areas of Borno state, where the IDP population is now well over 1.6 million," it said.
The IOM said the majority of those displaced by the violence (92%) now live in host communities while the remainder live in camps or camp-like sites, adding that the victims were in dire need of food and shelter.
"Many IDPs, especially in host communities, have yet to receive basic items including food and shelter," said Enira Krdzalic, IOM Nigeria Chief of Mission.
"It is very important for the authorities and humanitarian partners to speed up the delivery of adequate assistance to these people," she added.
Attacks by Boko Haram, which seeks to impose a strict Islamic system in northern Nigeria, have killed at least 15,000 people since 2009.
The extremists have carried out deadly ambushes across Nigeria's borders and in recent weeks suicide bombers, many of them women, have staged several attacks in Nigeria, Cameroon and Chad.
An 8,700-strong Multi-National Joint Task Force, drawing in Nigeria, Niger, Chad, Cameroon and Benin, is expected to deploy against the insurgents soon.