An Australian man faces the prospect of three years in jail in Japan after a desperate bid to track down his two young children, who were taken by their mother in May without his consent.

Scott McIntyre, an Australian freelance journalist based in Tokyo, has been charged with illegal entry, which under Japanese law carries a maximum penalty of three years in jail, or 100,000 yen ($1327).

"I'm desperately worried for Scott's future," said Mr McIntyre's mother Lynne. "He's been through so much already. If he gets three years it will completely destroy him."

Mr McIntyre, 45, has been living in Tokyo with his wife since 2015. After the breakdown of their marriage, the children went to stay with their grandparents for a night and never returned.