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We show that for all $\ell, k, n$ with $\ell \leq k/2$ and $(k-\ell)$dividing $n$ the following hypergraph-variant of Lehel's conjecture is true.Every $2$-edge-colouring of the $k$-uniform complete hypergraph$\mathcal{K}_n^{(k)}$ on $n$ vertices has at most two disjoint monochromatic$\ell$-cycles in different colours that together cover all but at most$4(k-\ell)$ vertices. If $\ell \leq k/3$, then at most two $\ell$-cycles coverall but at most $2(k-\ell)$ vertices. Furthermore, we can cover all verticeswith at most $4$ ($3$ if $\ell\leq k/3$) disjoint monochromatic $\ell$-cycles.

Partitioning $2$-coloured complete $k$-uniform hypergraphs into monochromatic $\ell$-cycles