Head of the King Juan Carlos University in Madrid since 2013, Fernando Suarez has been accused of numerous counts of plagiarism, perhaps over as much as 10 years.
Suarez was forced to quit his position on the permanent commission of the conference of Spanish university chancellors, which said it was due to "information published about the presumed plagiarism".
He is suspected of copying work by students as well as colleagues, both at home and abroad.
One person Suarez is suspected of having copied is French historian Bernard Vincent, who claims his work appeared in an article the Spaniard sent to the University of Santa Barbara in California.
"I'm absolutely indignant. It's scandalous," Vincent told AFP.
"He copied two of my paragraphs on the repression carried out under the Inquisition in Spain, but he borrowed entire pages from five other colleagues.
"Of the 30 pages in his article, 26 or 27 were 'borrowed'." Last month, Suarez had written to his university's board claiming to be the victim of "defamation" and "harassment".