Reportedly, several bishops have said they will not be present when the pope visits the archbishopric in the capital Nicosia or attend any official engagements, even though the Cypriot church has welcomed the June 4-6 visit.
'There is democracy in the Church, there is freedom of speech and people can give their opinion, but they cannot do as they please,' he told reporters in response to media reports of a divided clergy.
He said the Cypriot Church would welcome the pope as a guest of the government and urged the faithful to do the same.
'The Holy Synod has decided and decisions by the Synod are obligatory. The Church is just but strict; whoever doesn't like it can stay in their own home. That's my opinion.'
Archbishop Chrysostomos II criticised one of his own, influential Limassol Bishop Athanasios, for publicly opposing the papal visit.
Members of two religious groups have already called on the attorney general to arrest the pope as soon as he sets foot in Cyprus for his alleged 'cover-up' of paedophile crime by Catholic priests.
And there are unconfirmed reports that people incensed over the paedophilia scandal will demonstrate against the pontiff.
Last week the synod issued a circular that was read out in churches across the island assuring the faithful that the pope's visit would not compromise Orthodoxy and calling for calm.'We urge all of you to keep quite and calm,' the letter said. 'Close your ears to any irresponsible exhortation calling you to respond by protesting the pope's visit.'
The visit to overwhelmingly Orthodox Cyprus is seen as an opportunity to bring the faiths closer together, Roman Catholic Church officials have said.
SIC: ST