The call comes nine months after the Holy See and Beijing reached an agreement ending three decades of division in China between an "official" Catholic Church recognized by the government and an unofficial one loyal to the Vatican.
Under the pact, China agreed to give the Pope final approval on the appointment of bishops, while clergy affiliated with the unofficial church would be required to register with authorities.
Problems have arisen, however, because, according to the Vatican, most priests and bishops trying to register are asked to sign a document affirming "the principle of independence, autonomy and self-administration of the church in China", Efe news reported.
Some clergymen see that affirmation as undermining their links to the Pope and the universal church.
Published on Friday, the Vatican's pastoral guidelines concerning the civil registration of clergy in China provide detailed instructions for dealing with the dilemma as the church continues talks with Beijing in pursuit of "a formula that, while allowing for registration, would respect not only Chinese laws but also Catholic doctrine".
"If a bishop or a priest decides to register civilly, but the text of the declaration required for the registration does not appear respectful of the Catholic faith, he will specify in writing, upon signing, that he acts without failing in his duty to remain faithful to the principles of Catholic doctrine," the text says.
At the same time, the Vatican expressed understanding and respect for "the choice of those who, in conscience, decide that they are unable to register under the current conditions", while urging Chinese authorities not to penalize non-compliant clergy.
"The Holy See asks that no intimidatory pressures be applied to the 'non official' Catholic communities, as, unfortunately, has already happened," the document said.
From the Vatican's standpoint, the independence of the Catholic Church in China is "relative to the political sphere, as happens everywhere in the world".
"To affirm that for the Catholic identity there can be no separation from the successor of Peter does not mean making the local church an alien body in the society and the culture of the country in which she lives and works," the Vatican said.
( With inputs from IANS )