The First Doctor told Ian Chesterton that they were "already in the next universe but one" when the TARDIS landed on Skaro, thus making the human's preoccupations about his planet irrelevant according to the Doctor. (PROSE: Doctor Who in an Exciting Adventure with the Daleks)
The Dalek Emperor discovered that Earth existed in "the next universe but one" upon circling Andromeda; this was always a "blind spot" for Skaro, as Earth was part of another universe hidden due to skycurve, (COMIC: The Road to Conflict) Lodian explaining that when he and Yvric discovered Earth, it was nine galaxies away from Skaro, (COMIC: Legacy of Yesteryar) which existed deep in Hyperspace. (COMIC: Genesis of Evil)
The amnesiac Eighth Doctor once mentally referred to the Klade as coming from the "next universe but one". The Klade came from one of the galaxies of the far future. (PROSE: Father Time [+]Loading...["Father Time (novel)"]
Behind the scenes
According to AUDIO: Quinnis, which picked up the thread of The Edge of Destruction of the First Doctor and Susan having travelled to the fourth universe, N-Space was the third universe. Logically, if the Doctor's statement in Doctor Who in an Exciting Adventure with the Daleks is to be understood within the same framework, this would make the "next universe but one" the fifth universe (as "next but one" is an English expression, meaning "the one after the next one," i.e. Skaro is two universes away from Earth).
Although it is likely this is antiquated scientific terminology which referred to galaxies as "island universes", Genesis of Evil, another Dalek story written in he 1960s by David Whitaker, also posited that Skaro did not quite exist within the Doctor's universe, placing it in hyperspace.