Given a positive integer $n$ and a nonnegative integer $k$ with $k\leq n$, we denote by $\mathcal{A}(n,k)$ the class of all $n$-by-$n$ $(0,1)$-matrices with constant row and column sums $k$. In this paper, we show that the Bruhat order and the secondary Bruhat order coincide on $\mathcal{A}(n,k)$ if and only if either $0\leq n\leq 5$ or $k\in\{0,1,2,n-2,n-1,n\}$ with $n\geq 6$.