When, in 1553, Simão Rodrigues, the first provincial of Portugal, was summoned to Rome to answer charges made against his administration, the visitor, Nadal, assigned him Carneiro as a companion.

The pope had given them an order of obedience to accept consecration, and Loyola acquiesced, considering that the dignity carried with it hardship and suffering rather than honour.

Unable to enter his missionary field of Ethiopia, Carneiro set out for Portuguese India and landed at Goa.

Not able to fulfil his original assignment, he received the brief Ex Litteris carissimis from Pope Pius V in 1566 appointing him apostolic administrator for the Portuguese missions in Japan and China.

[clarify] His work there was rewarded when the Diocese of Macau was established in 1576 by Pope Gregory XIII.