The public prosecutor ordered the arrest of Abd al-Karim Sabra, editor-in-chief of privately owned Al-Hurriya (Freedom), late on Monday.
Publication of Al-Hurriya was earlier suspended, the state news agency SABA reported.
Al-Hurriya is the third newspaper in the Arab world to publish the caricatures.
SABA reported that Sabra will be "prosecuted because his newspaper took the initiative of republishing cartoons that are offensive to the prophet".
The syndicate of Yemeni journalists said in a statement that Sabra's union membership has been suspended "because he deliberately ignored professional norms".
The Yemeni authorities said the cartoons were considered "harmful to the Islamic faith and derogatory of a monotheistic religion or humanitarian belief".
An information ministry spokesman said: "The ministry is very protective of press freedom, but it must be within the bounds of the law."
The weekly publication carried the cartoons, which were first published by Danish newspaper Jyllands-Posten last September, in its Saturday edition.
Two Jordanian tabloid editors face trial for printing the cartoons, which included depictions of the Muslim prophet as a knife-wielding beduin and another with a bomb-shaped turban.