Gut bacterial translocation to the blood may play an important role in the development of insulin resistance in type 2 diabetes. Here, we performed an interventional randomised control study to investigate whether probiotics could reduce bacterial translocation and cause changes in the gut microbiota. Seventy Japanese patients with type 2 diabetes were randomised to two groups: the probiotic group drank Lactobacillus casei strain Shirota-fermented milk, while the control group ingested no probiotics. The trial was conducted for 16 weeks. At baseline, 8 and 16 weeks, the gut microbiota composition in feces and blood, fecal organic acids, and other biochemical parameters were measured. At the end of the study, the fecal counts of the Clostridium coccoides group and Clostridium leptum subgroup in the probiotic group were significantly higher than in the control group. As expected, the fecal counts of total Lactobacillus were significantly higher in the probiotic group. Intriguingly, the total count of blood bacteria was significantly lower in the probiotic group. However, fecal organic acids were comparable between the two groups. Our results showed that probiotic administration reduced bacterial translocation and altered the gut microbiota in Japanese patients with type 2 diabetes mellitus.