Koïchiro Matsuura, director-general of Unesco, this week rejected an academic boycott of Israel.
His comments came as two Parisian universities wrestled with the boycott issue, which erupted in Britain last year after Israeli military operations in the Gaza Strip and the West Bank.
Mr Matsuura said: "We must do everything to preserve the dialogue between the various scientific communities and international academics."
The administrative council of Paris University-6, Pierre-et-Marie-Curie, passed a motion that included a call for "non-renewal of the EU-Israel [research] agreement of association".
As Israel reeled from a double suicide bombing in Tel Aviv and threatened to close three West Bank universities it views as nurseries of terrorism, prominent intellectuals denounced the "non-renewal" motion at a demonstration organised by the Union of Jewish Students of France. Protesters included Bernard Henri-Lévy and Nobel laureate Claude Cohen-Tannoudji.
Politicians who opposed the motion included former education minister Jack Lang, who is an honorary doctor of Jerusalem University. The education ministry called the motion "inappropriate". It said that the universal dimension of higher education and scientific research required they should be treated separately from issues of foreign policy.
University president Gilbert Béréziat said that the motion had been misunderstood. The council had dismissed any idea of a boycott and had mandated him to "establish contacts with heads of Israeli and Palestinian universities to develop inter-university cooperation and work for peace".
The vote to cease EU-Israel cooperation was intended as criticism of the Israeli government's policies, he said.
The administrative council of Paris-7 University, Denis-Diderot, which shares a campus with Paris-6, rejected a similar proposal for "suspension of scientific exchanges with Israeli universities", voting instead "in favour of a reinforcement of agreements with all universities throughout the world".