A lack of new students and teachers has led to the decision to close the Scotus College.
There are currently only nine students at the seminary in Bearsden, near Glasgow, down from 55 when it opened in 1993.
The latest figure is a huge fall from the 136 candidates who studied at Chesters College, which stood on the Scotus site, and Gillis College, in Edinburgh, 25 years ago – and an even bigger drop from the 193 students at Scottish seminaries in 1978.
The three resident priests who teach at Scotus College – with a further 20 teaching staff – will return to their dioceses. New trainee priests will now go the Scots College in Rome.
The Very Rev William McFadden, the rector of the college, said the decision had been taken because of a lack of candidates and a shortage of ordained priests to carry out training. He blamed the fall in number of candidates on changing modern attitudes.
"It would appear that every institution that is looking for some sort of commitment from people is suffering from a lack of people," he said.
"There is a sense that people are not putting themselves forward because of the priest's lifestyle. But, that said, there is still a steady number of people coming forward for priesthood."
Scotus College, which takes its name from the Scottish medieval theologian John Duns Scotus, first came under the threat of closure in 2002, but the Church decided to retain the seminary, which had 37 students at the time, and instead closed its Royal Scots College in Salamanca, Spain.
Announcing the closure yesterday, the Bishops' Conference of Scotland said it was "a matter of regret" but that it would "allow bishops to take advantage of the spiritual, cultural and academic opportunities available in the Roman Pontifical Universities and other institutes of higher learning at the heart of the Church".
It added, however, that should the number of candidates for the priesthood increase, it would reassess the situation.
Liz Leydon, editor of the Scottish Catholic Observer, said: "With the number of students attending Scotus College and the Scots College in Rome at the moment, it would seem a sensible decision, rather than staff two colleges.
"Nonetheless, it comes as quite a disappointment. It's a sad day when Scotland won't have a seminary for the first time in almost 300 years."
She said the Vatican's stipulation on the minimum number of priests working as full-time teaching staff meant that the ratio of students to teachers at Scotus College was considered unfeasible.
Father Andrew McKenzie, the director of Priests for Scotland, which promotes the priesthood, said the number of students was on the rise. "The principal problem regarding the continuance of the seminary is the provision of faculty," he said.
"It's becoming increasingly difficult to cover all the subjects required. Therefore, when a course can be provided in Rome, it obviously has an appeal because there's no need for Scotland to provide that."
Acknowledging that the number of students training for the priesthood was low, Fr McKenzie insisted the trend was upwards.
The shift to Rome is expected to be completed in time for the next academic year.