Mexico's Panamerican University said yesterday it had reviewed the president's 25-year-old thesis and found five types of "treatment of the ideas of others."
They included "textual reproductions of citations without footnotes or mention in the bibliography," it said in a statement.
In other cases, Pena Nieto reproduced passages from works referenced in his bibliography without indicating they were citations, or "ambiguously or imprecisely" credited the author, it said.
The assessment came after the website Aristegui Noticias concluded that 197 of the 682 paragraphs in Pena Nieto's thesis were plagiarized, based on analysis and speaking with professors.
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However, it has consulted the country's largest university, the National Autonomous University of Mexico (UNAM), on how to proceed in the "unprecedented" case, it said.
The controversy arises as Pena Nieto's popularity is at an all-time low, with only 23 per cent of Mexicans holding a positive opinion of the leader, according to a recent poll published by the newspaper Reforma.
The website behind the investigation is headed by well-known Mexican journalist Carmen Aristegui, who in 2014 revealed Pena Nieto's wife, former soap opera star Angelica Rivera, had bought a USD 7 million Mexico City mansion from a government contractor.