Let $G$ be a finite cyclic group. Every sequence $S$ of length $l$ over $G$ can be written in the form $S=(x_1g)cdotldotscdot(x_lg)$ where $gin G$ and $x_1, ldots, x_lin[1, ord(g)]$, and the index $ind(S)$ of $S$ is defined to be the minimum of $(x_1+cdots+x_l)/ord(g)$ over all possible $gin G$ such that $langle g rangle =G$. Recently the second and the third authors determined the index of any minimal zero-sum sequence $S$ of length 5 over a cyclic group of a prime order where $S=g^2(x_2g)(x_3g)(x_4g)$. In this paper, we determine the index of any minimal zero-sum sequence $S$ of length 5 over a cyclic group of a prime power order. It is shown that if $G=langle grangle$ is a cyclic group of prime power order $n=p^mu$ with $p geq 7$ and $mugeq 2$, and $S=(x_1g)(x_2g)(x_2g)(x_3g)(x_4g)$ with $x_1=x_2$ is a minimal zero-sum sequence with $gcd(n,x_1,x_2,x_3,x_4,x_5)=1$, then $ind(S)=2$ if and only if $S=(mg)(mg)(mfrac{n-1}{2}g)(mfrac{n+3}{2}g)(m(n-3)g)$ where $m$ is a positive integer such that $gcd(m,n)=1$.
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