For some years he privately took up issues of allegations of atrocities and starvation with the Indonesian military leaders, but came to realise that he was being ignored. So in 1981 he changed tactics. He now made his complaints public by writing letters overseas and then giving his permission for them to be published in newspapers and through the media, so that the world community, unaware of what was happening in the closed territory, would come to learn of the killings by the Indonesians. In particular he criticized the forced conscription of 50,000 men and boys to form a human chain to help crush the Fretilin resistance, and later denounced the Indonesian army for war crimes, in particular the massacre of 500 women and children at the Shrine of St Anthony at Lacluta in September 1981.
He was reprimanded by the military and infuriated President Suharto. Never before had an East Timorese so publicly exposed and humiliated the Indonesian Armed Forces. His response was: "I feel the irrepressible need to tell the whole world about the genocide being practised in Timor so that, when we die, at least the world will know we died standing".
Meanwhile he continued to highlight the evidence of massive starvation in the resettlement camps and gave his support to his priests who sought to stand alongside the people. Desperately he wrote to the Pope requesting a special audience, to which the Vatican responded that it was neither timely nor necessary. For Mgr da Costa Lopes this was one of his hardest blows. He went on, in a letter to Australia, to accuse the Indonesian military of mass murder, and anticipated widepead famine unless large food supplies were urgently imported. His predictions were proved correct.
Former Australian Prime Minister Whitlam, far removed from East Timorese reality, called the bishop "a liar, who was simply stirring up trouble". However his denunciations proved so controversial and supported by outside agencies that Indonesia could no longer tolerate them.
General Benny Moerdani was suspected of persuading the Papal Pro-Nuncio in Jakarta, whom he was suspected of being close to, to advise the Pope to request the resignation of the Apostolic Administrator. This happened in May 1983, when Mgr da Costa Lopes retired, painfully leaving his native land to live in Lisbon where he died on February 27, 1991. Lopes was succeeded as Apostolic Administrator by Carlos Felipe Ximenes Belo.
Martinho da Costa Lopes grew up in an era when the Portuguese church in what was then Portuguese Timor cooperated closely with the Portuguese colonial government, but was less strongly linked with the people, of whom only 28% were Catholic in 1975. In spite of this grounding and in spite of his being in his 60s, he oriented the church towards support for the Timorese people fighting in the mountains and for those priests (Portuguese and Timorese) who had gone to live in the mountains with them. In 1981 the people's language, the Tetum language, was made an official language of the Catholic liturgy in Timor.
The decision by the Vatican to force him to leave was made over the heads of the Timorese clergy, many of whom wrote to the Pope opposing it. Mgr da Costa Lopes paid for his outspoken criticism of Indonesian actions in East Timor with his job.
However his name remains associated with a historic re-orientation of the Timorese church towards the local culture and people. This new and indigenous church achieved, during these six years, a numerical growth which centuries of work by Portuguese missionaries had never managed in East Timor.