Fernando Suarez, who heads the King Juan Carlos University in Madrid, is accused of repeatedly copying other people's work without giving credit.
On Thursday, he was removed from his chairmanship on a national education commission.
Mr Suarez has said he is the victim of defamation and harassment.
The permanent commission of the conference of Spanish university chancellors said on Thursday that Mr Suarez was leaving due to "information published about presumed plagiarism".
He has been accused of copying other historians' work and that of his students, over a period of up to 10 years.
One article published under his name was said to consist of 70% copied-and-pasted words from another person's book.
The French historian Bernard Vincent told the AFP news agency Mr Suarez had borrowed paragraphs from his work, describing it as "scandalous".
He said: "I'm absolutely indignant."
Last month, the university Mr Suarez heads had informed students that the campus had installed a system called Unplag to monitor submitted assignments for plagiarism.
An email sent to 40,000 students stated that the new programme would help uphold standards of integrity, academic honesty and independent thinking.
Students have set up at least nine separate petitions calling for Mr Suarez to resign from the top job at the university. Together they have collected tens of thousands of signatures.
One pointed out: "Plagiarism is grounds for any student to be suspended immediately."
The chancellor of a Spanish university where students were told their work would be monitored for plagiarism has himself been accused of plagiarising.