Pope Francis yesterday called for all Chinese Catholics to reconcile, while admitting that a historic deal with Beijing on nominating bishops may have caused "confusion".

"I now invite all Chinese Catholics to work towards reconciliation," the pope wrote in a message to Roman Catholics in the world's most populous country.

Saturday's deal has paved the way for rapprochement between the Vatican and the Communist country, despite the fears of some in the persecuted underground Church.

"Some feel doubt and perplexity, while others sense themselves somehow abandoned by the Holy See," the pope wrote.

"I am aware that this flurry of thoughts and opinions may have caused a certain confusion and prompted different reactions in the hearts of many."

Shortly after the deal, Francis recognised seven clergy appointed by Beijing, which has not had ties with the Vatican since 1951.

Yesterday, he called on the bishops to publicly reunite with the Vatican.

"Regrettably, as we know, the recent history of the Catholic Church in China has been marked by deep and painful tensions, hurts and divisions, centred especially on the figure of the bishop," he wrote.

“I ask them to express with concrete and visible gestures their restored unity with the Apostolic See."

There are an estimated 12 million Catholics in China, divided between a government-run association whose clergy are chosen by the Communist Party and the unofficial church which swears allegiance to the Vatican.

Pope Francis has sought to improve relations with China since he took office in 2013, but previous attempts foundered over Beijing's insistence that the Vatican give up recognition of Taiwan and promise not to interfere in domestic religious issues.

The Holy See is one of only 17 countries that recognise Taiwan, officially known as the Republic of China, instead of having diplomatic ties with Beijing.

"I hope that a new phase can be opened in China, which helps to heal the wounds of the past," the pope wrote.

The deal's aim is "to support and advance the preaching of the Gospel, and to reestablish and preserve the full and visible unity of the Catholic community in China."

The deal was signed as churches have been destroyed in some Chinese regions in recent months, and there has been a clampdown on Bible sales.