A survey of Echinococcus multilocularis infections in pet dogs in Japan from 1997 to 2007 was conducted by testing for coproantigen reactivity, fecal taeniid eggs, and egg DNA. In Hokkaido, the only island where E. multilocularis is endemic in Japan, 18 of 4768 dogs (0.4%) excreted taeniid eggs that were positive for E. multilocularis DNA by polymerase chain reaction (PCR). Most of the dogs testing positive for egg DNA were kept free-range, but three dogs had been kept inside their owners' houses. In addition, 15 dogs were suspected to be infected based on the results of a coproantigen test. One dog, which was transported from Hokkaido to Honshu, the main island of Japan, was excreting taeniid eggs that were positive for E. multilocularis DNA by PCR. These results suggest the importance of proper pet management in disease prevention, even for dogs kept indoors, and they point out a possible means by which the parasite may be introduced into non-endemic areas through transport of infected dogs.