On Thursday the United States said it had withdrawn most of the troops it deployed in Nigeria earlier this year to help fight Islamist militant groups.
US and Nigerian forces launched a joint operation in the Lake Chad Basin area in December, carried out strikes on Christmas Day and deployed about 200 soldiers two months later.
Senior Islamic State leader Abu-Bilal al-Minuki was killed during the months-long mission, the report said.
General Dagvin Anderson said the operation had been successful and that IS' leadership in Nigeria had been "significantly degraded."
Maj.-Gen. Michael Onoja said intelligence-sharing between the two countries would continue, and Nigeria's military spokesperson said the withdrawal would "not affect our momentum in any way."
Major General Samaila Uba said US military personnel who were stationed in Nigeria before the Lake Chad Basin operation have remained in the country.
Earlier this year the US said it would deploy about 200 troops to support Nigeria's counter-insurgency efforts while stressing that its forces would not take part in ground combat.
Military cooperation between Nigeria and the US increased after Washington accused Nigerian authorities of not doing enough to protect vulnerable groups and alleged there was a "Christian genocide" in the country; Nigeria rejected the claim, saying the violence is complex and affects people from all communities.
Organisations monitoring political violence say most victims of the jihadist groups are Muslims because the militants mostly operate in the north, and jihadist groups continue to stage attacks, especially in north-eastern Nigeria.
Anderson said the joint operation disrupted the group's local command structure and its wider global network, limiting its ability to communicate, and analysts say around 90% of IS attacks now take place in sub-Saharan Africa with the Nigeria-based branch by far the most active.
Nigeria faces multiple security challenges beyond Islamist militants: banditry and criminal violence plague the country and have spread from the north into parts of central and southern Nigeria.