The actions of two new bishops – one illicitly ordained, the other fiercely loyal to the Pope – have deepened the freeze in relations between China and the Vatican. The Holy See's response suggests a fresh determination to stand up for Chinese Catholics' religious freedom.

It could have been a cause for celebration for the Vatican and the Chinese state. The ordination of Thaddeus Ma Daqin as an auxiliary bishop in Shanghai was approved by both Rome and the Beijing government-controlled Catholic Patriotic Association (CPA), and it might reasonably have been assumed that Ma would be a unifying figure. After all, many other so-called "open church" bishops have been able to reconcile membership of the CPA with the underground Catholic Church.

But at his ordination on 7 July, Bishop Ma dramatically declared that he was resigning from the CPA. "As I now serve as a bishop, I should focus on pastoral work and evangelisation," he said. "It is inconvenient for me to take on certain responsibilities. Therefore, from this day of consecration, it will no longer be convenient to be a member of the Patriotic Association." The reaction of the Chinese Government was swift. Ma was taken away by "unidentified" persons and was said to be staying at a seminary "for a retreat".

At around the same time, the Vatican issued a communiqué declaring illicit the episocopal ordination of a CPA cleric. Fr Joseph Yue Fusheng became Bishop of Harbin in north-east China on 6 July despite repeated requests by the Vatican to him "not to accept episcopal ordination without the pontifical mandate".

The acts of these two bishops – one obedient to the CPA, the other determined to defy it – have brought Sino-Vatican relations to a new low. Bishop Ma was committing an offence against the Chinese Communist Party (CCP) by leaving the state-controlled CPA, even though article 2 of the association's constitution states that membership is on a voluntary basis. But he was being faithful to Pope Benedict XVI's advice in his 2007 pastoral letter to Chinese Catholics that CPA membership was "incompatible" with Catholic faith. There has been international concern about Ma's fate. On 10 July, Shanghai Diocese posted a notice on its website rejecting rumours that he was under house arrest. The notice, however, did not refer to Ma as a bishop, and the following day the CPA announced that he was under investigation for seriously violating regulations.

Ma is not the first bishop to fall foul of the state authorities for his loyalty to Rome. Underground Bishop John Wang Ruowang of Tianshui, in the northern Gansu province, was removed last December, less than a year after his ordination. Two other bishops have long been missing – James Su Zhimin of Baoding, in Hebei province, for 15 years, and Cosma Shi Enxiang of Yixian, in Hebei province for 11 years. Many other clergy and laity loyal to Rome have suffered harassment.

There are around 12 million Catholics in China, about half of them members of open communities which have registered at the CPA, with bishops recognised by Beijing. The rest are in underground communities. In many cases, these coexist harmoniously with the CPA, especially where bishops are approved both by the state authorities and by Rome. Catholicism is growing steadily in China; there were some 22,000 baptisms last Easter alone.

Nevertheless, religious freedom has long been a burning issue. The constitution of the People's Republic guarantees religious freedom, but at the same time Beijing tries to make sure that religious ­activities are under its control. The 2012 Amnesty International Annual Report ­criticised this approach, stating that those who join religious communities without state sanction risked harassment.

Beijing's attitude is about retaining its absolute hold on power. Small religious bodies, including Protestant house churches without a clear structure or international leadership, are treated with less suspicion than the Catholic Church. The Vatican, as a sovereign city-state, is often viewed as a political entity. Its diplomatic relationship with Taiwan has been an excuse for Beijing to cold-shoulder the Catholic Church, especially now that China has become an economic giant.

In addition, the unity of the Church and the mutual support that parishes and dioceses give each other encourages the Chinese Government to see it as a huge single entity. Beijing is sensitive to the role played by the Church in the collapse of the former Soviet Union and the Eastern Bloc in the late 1980s; it knows the Catholic Church can be a dangerous opponent. A clause in the Chinese constitution states that "religious bodies and religious affairs should not be subject to any foreign domination". There is an historical reason for this – Christianity expanded in China with the colonial power in the Qing Dynasty – but it also has a resonance today in China's attitude to the Vatican.

There have been many high and low points in the diplomatic journey travelled by the Vatican and China in recent years. Beijing was responsible for a severe chill in relations when it sanctioned the illegal ordination of five Chinese bishops on the Feast of the Ephiphany in 2000, while Rome was the cause of China's displeasure when Pope John Paul II canonised 120 Catholics martyrs on 1 October, China's national day. Some of the new saints had been missionaries killed in the Boxer Uprising, a rebellion that fought foreign influences, including Christianity, between 1898 and 1901.

In recent years, within the Church there have been two contrasting approaches to the question of relations with China. One, led for many years by Cardinal Ivan Dias, when he was prefect of the Congregation for the Evangelisation of Peoples, counselled a softly, softly approach. Other prelates, led by Hong Kong Cardinal Joseph Zen, have argued that the Vatican should be tough and uncomprom­ising. Zen, who taught at several Chinese seminaries before being ordained a bishop in 1996, knows well the tactics of the Communists. Ma was a student of Zen when Zen taught at the Shanghai Sheshan Seminary, where Ma is now said to be confined.

Zen has publicly praised Ma's bravery. He headed a protest to the Chinese Liaison Office in Hong Kong to support Ma on 11 July, and celebrated a Mass last Monday with some 1,000 local faithful, for Ma and other clergy suffering persecution. Earlier this year, Zen said that the Congregation for the Evangelisation of Peoples should not adopt "a policy of compromise" when talking with Beijing. He retired as Bishop of Hong Kong in 2009, but continues to keep alive Catholics' battle for religious freedom.

With the retirement of Cardinal Dias last year, Archbishop (now Cardinal) Fernando Filoni was named prefect of the Congregation for the Evangelisation of Peoples. Filoni, who headed a Vatican "study mission" in Hong Kong from 1992 to 2001, has close contacts with the Catholic communities in China. He was responsible for the Congregation's forthright note about the illicit episcopal ordination in Harbin, a line echoed in the Holy See's communiqué a week later. Filoni's appointment, together with the naming of Hong Kong Bishop John Tong Hon as a cardinal, suggests a determination by the Vatican to give a renewed urgency to its work on behalf of China's Catholics.

Tong, a long time observer of the Church in China, combines diplomacy and steeliness in his approach. When China invited the then Coadjutor-Bishop Tong (but not Cardinal Zen) to attend the opening ceremony of the Beijing Olympics in 2008, Tong wrote a front-page article for the Vatican newspaper, L'Osservatore Romano, expressing his appreciation of the gesture but also listing the names of Chinese bishops being detained or harassed.

Tong's recent appointment as one of the three president-delegates of the October Synod on the New Evangelisation, and as a member of the Council of Cardinals for the Study of Organisational and Economic Problems of the Holy See, are marks of the esteem in which he is held by Rome. In fact, Hong Kong has a long history of acting as a bridge between the Church in China and the universal Church. It has also been the only Catholic community under Chinese rule that has been able to criticise openly cases of human-rights violations.

Religious and secular media around the world have taken a keen interest in the Vatican's efforts to bring about religious freedom in China. Yet the Church is only seeking the rights articulated in the country's constitution, and many international human-rights protocols. Pope Benedict gave great spiritual encouragement to Chinese Catholics when, in 2007, he designated 24 May as World Day of Prayer for the Church in China. He prayed for unity among them "to become ever deeper and more visible". With its growing role on the international stage, it is clear that China must fulfil its moral duty and allow Catholics to enjoy what are their constitutional rights.