The Observatory of Fundamental University Values and Rights was launched in Bologna last week by a gathering of European higher education figures.
The project is supported by the Association of European Universities, the Council of Europe and Unesco. It has €250,000 (£155,000) in financing from the Italian government and the foundation of Carisbo, a Bologna-based bank.
Among the founders are Fabio Roversi Monaco, former rector of Bologna; Andris Barblan, AEU secretary general; Guy Haug, who will be responsible for education and culture in the Council of Europe; and Kenneth Edwards, former president of the European Rectors Conference.
The observatory grew out of the Magna Charta of European Universities, which 430 rectors from Europe and elsewhere signed in 1988. The document set out principles for higher education institutions, especially independence.
"The observatory is the executive arm of the Magna Charta to make certain these principles are observed and promoted. It is not a tribunal, it looks at situations, makes proposals and forms an opinion - a kind of Amnesty International for higher education," Professor Monaco said.
He added: "We have no direct power. Our legitimacy is a direct result of our prestige."
The observatory is looking at the university system of Croatia, where each university faculty is independent and answers to the university ministry.
The observatory feels this undermines autonomy and leads faculties to vie for state funding. It believes Croatia should change its laws governing universities.
Dr Haug said: "Only universities with a single administration can make independent decisions and thus be truly autonomous. In countries where legislation is being prepared, we will monitor the situation."