It was the first time Tokyo had taken such a measure on the grounds it was needed to protect the passport-holder's life, the Asahi Shimbun and other news reports said on Sunday.
They said the foreign ministry on Saturday confiscated the passport of Yuichi Sugimoto, a freelance photographer who had planned to enter Syria on February 27 to cover refugee camps among other places.
But the 58-year-old, who has covered conflict zones in Iraq and Syria over the years, said he had no plans to enter areas controlled by ISIL, Kyodo News reported.
"Tonight, an official with the foreign ministry's passport division came and took my passport," Sugimoto told the Asahi.
"What happens to my freedom to travel and freedom of the press?"
The passport confiscation came in the wake of the beheadings of journalist Kenji Goto and self-styled security consultant Haruna Yukawa by ISIL.
It also comes as the Japanese government scored higher public approval ratings following Prime Minister Shinzo Abe's handling of the hostage crisis, polls published this week showed.
Japan's biggest daily Yomiuri found that support for Abe's government had risen to 58 percent from 53 percent in January.
The paper surveyed 1,054 people by telephone on Friday and Saturday for the poll, which was the first since the hostages were killed.