Scottish Opera has been without a music director since the abrupt departure of Emmanuel Joel-Hornak, who left the company only a month after he started work in September last year.
While the company, which is also facing delays to the opening of its £12.45m new foyer at its main Theatre Royal venue, is searching for a new musical leader Sir Thomas will "provide high level input on musical and artistic matters".
Sir Thomas, 69, began directing operas in 2003 and has directed four for Scottish Opera, Rossini's The Barber of Seville, and Mozart's The Marriage of Figaro, The Magic Flute and Don Giovanni.
Scottish Opera's Theatre Royal redevelopment was due to open in May but now the theatre will re-open for Scottish Opera's production of Madama Butterfly on May 21 with the foyer incomplete, due to "extremely poor weather over the winter." The new additions to the building will now open in July.
Alex Reedijk, general director, said: "Tom is a master of the artform and a talented musician and his phenomenal experience in the world of opera - singing, teaching and directing - will be a great asset to the company."
Sir Thomas said: "Working with Scottish Opera in a directorial capacity has allowed me to confirm a lot of what I'd already suspected.
"There is a spirit and willingness to collaborate that is hard to find anywhere. I've loved being a part of that feeling and it makes me very happy to accept an advisory position with the company and play a part in its future."