In Wednesday's incident, the 38-year-old woman, who was in the sixth month of her pregnancy, was being driven to a hospital near the western city of Osaka after she suffered from stomach cramps and bleeding, according to Kyodo News agency and other local media.
Nine hospitals closer to her home in Nara prefecture (state), over 40 kilometers (25 miles) away, had earlier refused to admit her, saying they were full, the reports said.
Her water broke two hours into the journey. Ten minutes later, the ambulance collided with a minivan.
"This is a very grave incident," Heath Minister Yoichi Masuzoe told public broadcaster NHK late Wednesday. "The Health Ministry will conduct a thorough investigation," Masuzoe said.
Police were quoted as saying they were not sure the accident caused the woman's miscarriage. The woman and ambulance staff were not injured in the accident.