"We are becoming increasingly concerned by the growing role of clerics in Russian society, by the church's penetration into all facets of social life," several scientists, including two Nobel Prize winners, said in an open letter to Putin.
The Russian Orthodox Church has enjoyed a dramatic revival in its fortunes since the collapse of the Soviet Union in 1991.
But the letter, the text of which was published in several national newspapers, implied criticism of the Kremlin chief for his overt sponsorship of church activities.
A former officer with the KGB, which treated priests as subversives, Putin says he is an Orthodox believer, and he turns out for major Orthodox festivals, often accompanied by a long retinue of senior state officials.
The signatories to the letter said giving preference to the Orthodox Church could upset the ethnic and religious balance in the vast country that is also home to up to 20 million Muslims, as well as followers of dozens of other faiths.
The signatories included Zhores Alferov and Vitaly Ginzburg, who have won Nobel Prizes for science, and eight other distinguished scientists who are senior members of the Russian Academy of Sciences.
"The Constitution of the Russian Federation declares that our state is secular," the letter said.
The fresh concern about the Orthodox Church's mounting influence was triggered by a proposal to teach Orthodox studies as part of the standard school curriculum and to recognize theology as a science.
"One could wonder, why on earth theology -- a set of religious dogmas -- should be regarded as a science?" said the letter.
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