We report a case of a 79-year-old woman with an unusual salivary gland tumor that developed at the junction between the soft and hard palates. The tumor consisted of sialadenoma papilliferum (SP) with areas of an epithelial-myoepithelial carcinoma (EMC) component and a high-grade carcinoma component. There were also transitional regions among the SP, the EMC and the high-grade carcinoma components. The high-grade carcinoma component, which was similar to invasive micropapillary carcinoma of the breast, infiltrated into the right parapharyngeal space and metastasized to the lungs and cervical vertebrae. The high-grade carcinoma cells were positively immunostained for p53 protein. SP has been considered to be a benign tumor with exceptionally good prognosis, and, to the best of our knowledge, there has never been a confirmed case of malignant SP. This is the first report of SP with a definite malignant component.