I suppose it depends on what you mean by "substantial", but the Bump tunnel was a reasonable length. There was also a tunnel on Henry's (if I recall correctly) tramway out of Forrest.Australian Portland Cement had a tunnel in their Fyansford line.
Yep, that's the one I was thinking of. Just to show I can think of things outside of Gippsland.
And before anyone says it, I'm aware there was a tunnel near Powelltown, but I'm not aware of it being a particularly "substantial" one (the bump).
I probably should've reworded the question when I realised The Bump was a possible answer. I know it was a reasonable length. But I've never seen photos of it or had a look myself when I've driven over it. I had a feeling there may be other tunnels on various tramways, but I sort of assumed such tunnels would be somewhat roughly constructed. But perhaps not.
Anyway, I got the answer I was hoping for.