Speculation has flourished about a possible historic meeting between Russia's Patriarch Alexiy II and Pope Benedict XVI after both sides indicated they were open in principle to healing a centuries-old rift between Western and Russian Christianity.
Russia is by far the biggest Orthodox Christian church and has undergone a big religious revival since the demise of the atheist Soviet Union. President Vladimir Putin, once a KGB spy, is now open about his Orthodox faith.
"Stopping us from restoring relations are some unsolved issues between our churches," Alexiy told the Polish daily Dziennik in an interview published on Monday.
"We have many questions about the missionary and charitable activities of Catholic monks and clergy in Russia and CIS (former Soviet) countries."
The Russian Orthodox Church, by far the dominant religion in Russia, has sharply criticised the Vatican for creating new dioceses on its turf and has accused Catholic priests of attempting to poach Orthodox believers as converts to Rome.
Alexiy said some Catholic clerics "started to see the ex-Soviet Union as a spiritual desert to be dealt with".
The Catholic Church says it is only doing what is necessary to attend to the needs of Russia's estimated one million Catholics, mostly of East European or German origin, who were neglected during decades of religious persecution in the Soviet Union.
"We have always said that a Russian visit of (former) Pope John Paul was possible only when all the problems between our churches were resolved. Unfortunately, it has not happened until now," Alexiy said.
"In Russia and Ukraine, Catholics always treated the Orthodox believers more as enemies than as brothers in faith ... the activities of Catholics in Russia have created many challenges for the dialogue of our churches."
"These matters need to be resolved".
In particular, Alexiy criticised Catholic shelters which he said brought up orphans from Orthodox families in the Catholic tradition, saying this "is hurting us exceptionally".
Archbishop Tadeusz Kondrusiewicz said last October at a farewell news conference after 16 years heading the Catholic Church in Russia that the Orthodox "could have been better to us", adding he never sought to convert Orthodox Christians.
Christianity split into two branches in the Great Schism of 1054, when the Orthodox Church broke away from the Roman church in a row over papal authority and the insertion of a disputed clause into the Creed, the central statement of Christian faith.