Jamal Amer, editor-in-chief of the independent weekly newspaper al-Wassat, said on Tuesday armed men blindfolded him, forced him into a military car and took him to a remote area outside the capital Sanaa where they beat him.
"They warned me about slandering state officials and questioned me about writers and editors at the newspaper, and about our sources and funding," he said.
Officials were not immediately available for comment.
Al-Wassat has published several stories criticising President Ali Abdullah Saleh's government and the way it handled last month's riots over fuel price rises, in which 22 people were killed.
The cabinet later revised its decision and cut fuel prices.
Yemen's Journalists' Syndicate condemned the kidnapping as a dangerous action hostile to freedom of the press and journalists.
Earlier this year, Saleh pardoned a journalist imprisoned for slandering the Arab state's ruler and supporting a slain anti-US rebel cleric.