Several years ago I submitted "There were twelve Disciples" to The Cyber Hymnal, where it resides to this day, but neither they nor I have been able to find anything on its authorship. (Gargoyle's date of no later than 1958 is helpful but not surprising; I learned it about a decade later, I think, probably in a Presbyterian context.)

The Cyber Hymnal shows John Newton as having written a hymn entitled "Zaccheus climbed the tree", but this is unlikely to be the one you're thinking of.

Haruo