In an interview with Itar-Tass news agency, Alexiy also welcomed what he called Russia's "second baptism" -- the revival of the Orthodox Church since the demise of the officially atheist Soviet state in 1991.
"I believe in our people, in its spiritual powers and mind, in its age-old devotion to spiritual and cultural tradition," he was quoted as saying.
"We have to make the faith the centre of thoughts, feelings and deeds of any person who wants to be an Orthodox Christian."
But Alexiy, known for his tough line on non-traditional faiths, made clear Orthodoxy should enjoy precedence over other Christian confessions. "The church's renaissance is just beginning," he told the agency.
"The Patriarch could not fail to note there is a certain danger from pseudo-religions, from spiritually alien 'conquistadors' who are ruining, willingly or unwillingly, the spiritual integrity of Russian society," Tass said.
Alexiy said Russia's 1997 law "On freedom of conscience and religious organisations," condemned as discriminatory, by human rights groups, the United States and the Vatican, had not fully eradicated the threat of such "alien" religions.
But he added that the law did help the nation to "protect itself against attempts to impose an alien will on it."
The law, which identifies Orthodox Christianity, Islam, Buddhism and Judaism as Russia's traditional faiths, requires religious groups to re-register by a December 1999 deadline and sets a 15-year waiting term for those deemed "non-traditional."
Unregistered groups lack full legal rights and cannot conduct missionary or educational work. The law gives the courts the right to disband any religious group they find guilty of inciting hatred or intolerant behaviour.
The influential Orthodox Church and many of its defenders among parliamentarians and top officials say the law is needed to halt the spread of dangerous sects trying to exploit a spiritual vacuum left after the fall of the Soviet Union.
But critics accuse the church, still rebuilding itself after decades of official harassment and persecution, of wanting to monopolise Russia's spiritual life. They say the law breaches Russia's constitution, which proclaims a secular state where all religions are equal.
A case has been filed under the new law against the Jehovah's Witnesses in Moscow. Prosecutors want to ban the group, saying it breaks up families and sows religious hatred.
Other religious groups have come under pressure since the new law was passed and often face similar accusations of anti-social activity and brainwashing naive Russians.