On its system traffic light ratings, the commission ranked the scheme amber-red - the second lowest rating - indicating "significant improvements" were required.
To date, the Department for International Development (Dfid) has spent £102 million on supporting education in 10 of Nigeria's 36 states, with a further £126 million committed to 2019.
However, the commission found that around a third of the eligible children - an estimated 3.7 million - were still not in school, while those that were received little by way of education.
"We are concerned by the very high numbers of out-of-school children and the very poor learning outcomes in nine of the 10 Nigerian states supported by Dfid," it said."Dfid's education programme in Nigeria operates in a very challenging environment, with too few effective teachers, poor infrastructure and unpredictable state funding all contributing to poor learning outcomes for pupils in basic education.
"Our review indicates no major improvement in pupil learning."
The findings will further add to the pressure on ministers over the aid budget, with many Tory MPs strongly opposed to David Cameron's commitment to maintain overseas aid at a time of spending cuts at home.
ICAI chief commissioner Graham Ward said: "The communities we spoke to in Nigeria want their children to become self-reliant by learning to read and write.
"In our view, Dfid's programmes will only become sustainable when they can routinely help to unlock state governments' budgets to fund the required improvements both adequately and equitably."
A spokesman for Dfid said: "This was a limited enquiry in that the team only visited one per cent of schools, most of which were in only one state in Nigeria, and they did not take into account the most recent evidence of the projects' progress. However, we will carefully review the report's recommendations and respond in due course."
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