The original statement was released late Wednesday after talks between Nigeria's defense minister and Pakistan's chief of staff in the Nigerian capital of Abuja, the BBC reported.
The statement, issued by Nigeria's Ministry of Defense, quoted chairman of Pakistan's joint chiefs of staff Gen. Muhammad Aziz Khan as saying Pakistan "is working out the dynamics of how they can assist Nigeria's armed forces to strengthen its military capability and to acquire nuclear power."
Nigerian officials now say Khan was only discussing "military co-operation" with Defense Minister Rabiu Musa Kwankwaso.
Pakistan's Foreign Minister Khursheed Kasuri told journalists in Islamabad the original reports were "unadulterated rubbish."
Pakistan has already taken considerable heat since its top nuclear scientist last month admitted to passing secrets to Libya, Iran and North Korea.