Type VI secretion systems (T6SSs) are versatile macromolecular machines in about 25% of the Gram-negative bacteria. The genome of Xanthomonas perforans (Xp), a pathogen causing bacterial leaf spot disease on tomato and pepper, carries two gene clusters (~40kb), T6SS-I and T6SS-III, whose predicted products have homology with T6SS-associated gene products from other bacteria. Despite evolutionary conservation of large T6SS clusters, the contribution of these large clusters towards the infection strategies of X. perforans remains investigated. Here, we present evidence that T6SS-III plays an important role in the pathogenesis of Xanthomonas perforans on tomato plants. We constructed a knockout mutant of X. perforans carrying an in-frame deletion in the core T6SS-III gene, icmF3. In planta growth assays using Xp?icmF3 mutant and the wild type strain, individually and in competition, indicated that the mutant had a significant advantage in terms of growth in tomato plants as well as degree of disease severity. Xp?icmF3 mutant also exhibited higher disease index in seedlings, indicating possible role of T6SS-III in seed to seedling disease transmission. Delay in overall disease symptom development along with slower in planta growth might provide a significant fitness advantage to a hemi-biotrophic pathogen. Our results demonstrate possible role of T6SS in contributing towards latent infection period of a pathogen.