We can say "We'll take (a) five minutes' break" with or without the article, even though we can say only "We'll take a break" with the article. "A five-minute break" and "a five-minute rune" are fine,
'(A) five minutes' run" is not very natural with or without the article, although it's just about possible in a sentence such as "The pool is only (a) five minutes' run from here".