Prokaryotes and eukaryotes use diverse strategies to cope with invading mobile genetic elements, including programmed DNA elimination (PDE). In the ciliate Paramecium, elimination of transposable elements and their relics requires the PiggyMac (Pgm) endonuclease and its five PgmL partners, yet how this machinery is targeted to cleavage sites remains unclear. Here, we identified condensin I subunits in the proximity proteomes of Pgm and PgmL4. We show that they belong to a condensin complex that is essential for PDE and localizes to developing somatic nuclei. Depleting the development-specific subunits of this complex blocks DNA elimination, phenocopying a Pgm depletion. Developmental condensin is required for the correct nuclear localization of Pgm and some of the PgmLs. Moreover, Pgm and these PgmLs co-immunoprecipitate with condensin I. Our findings uncover functional and physical interactions between a eukaryotic DNA cleavage machinery and a specialized condensin complex that is critical for PDE in a non-dividing nucleus.