It would have been fairly uncommon.

The main language instruction that went on in Japan was actually in Latin, as it was necessary to allow converts to participate in mass (Dougill's book, referenced below, has some fascinating sections on the strange pidgin Latin that survived in Japan's small "hidden Christian" communities after contact with European priests was completely cut off). Rather than expect local people to learn Portuguese, or any other European language, potential missionaries underwent Japanese language training that was available in bases like Macao, using Japanese expatriates, and, after the imposition of the Sakoku edicts in the 1630s (which effectively closed Japan to Europeans and prevented Japanese from travelling overseas in more than the most limited ways), shipwrecked sailors as language instructors. One consequence of this was that the priests often learned a very low class, oddly accented form of the language which proved to be a barrier to their efforts to convert higher ranking Japanese.

This is not to say that the learning of Portuguese did not happen at all. The first Japanese baptised as a Christian, a man called Anjiro – a murderer who boarded a Portuguese ship to escape punishment for his crime (1546) – travelled as far as Goa and as a result of his immersion in the Portuguese world, learned some of the language – it took him about eight months, but there are variant accounts of how well he mastered it; the missionary Francis Xavier's companion Nicolò Lancilotto reported that at the end of that time Anjiro "still cannot speak [Portuguese] well, but since he is very discreet, he lets me understand him in a circumlocutional way."

Because Portuguese was the lingua franca of international trade in the Far East, others did follow. Boxer cites the journals of Richard Cocks, the head of the English factory in Japan from 1613-23, to make the point that "many Japanese spoke and wrote [Portuguese] with the greatest fluency," the language spreading largely as a product of the not uncommon intermarriage between Portuguese merchants and Japanese women in this early period. But of course Cocks was referring only to the Japanese he met in the course of his work as a trader in a port city. The language was certainly not remotely commonly spoken outside such locations.

This period was quite short-lived, moreover, since the Portuguese were expelled from Japan in the 1630s. Later, when only the Dutch among European nations were allowed to trade with Japan, a very small group of Japanese translators were allowed to learn Dutch and to visit the Dutch traders in their semi-isolation on an artificial island in Nagasaki harbour. Given the problems outlined in Silence, and after the crushing of the – quite serious – Shimabara Rebellion, which, however wrongly, was widely attributed to the spread of Christian ideas and influence, it was by this stage considered quite dangerous to allow free communication between Europeans and any other than carefully selected Japanese. The head of the Dutch legation was required to make an annual visit to Edo (Tokyo) and he did this in a sealed conveyance in order to minimise the disturbance that the advent of outsiders could cause.

The main reason for allowing translators to exist at all was to make it possible to create translations of Dutch scientific works, which had a major impact on a number of Japanese professions, especially medicine. This sort of translated information even had a special name, rangaku, meaning 'Dutch learning.'

I touch on some of these problems in an essay on the fate of Japanese sea drifters in the Pacific after the imposition of the Sakoku Edicts, here.

Sources

Boxer, The Christian Century in Japan

Dougill, In Search of Japan's Hidden Christians

Higashibaba, Christianity in Early Modern Japan

Laver, The Sakoku Edicts and the Politics of Japanese hegemony

Leupp, Interracial Intimacy in Japan: Western Men and Japanese Women, 1543-1900

Plummer, The Shogun's reluctant Ambassadors: Japanese Sea Drifters in the North Pacific