Andrei Safonov, editor in chief of the weekly "Novaya gazeta," is known as a critic of Transdniester's ruler, Igor Smirnov, whom he has accused of perpetrating human rights violations.
Smirnov is seeking a fourth term in office in elections scheduled for December 10.
Transdniester's electoral commission said Safonov's bid was denied because he had not met stipulations regarding the gathering of signatures to back his bid.
Safonov told RFE/RL's Romania-Moldova Service that he "would not rule it out that the decision is the result of clear political involvement."
Safonov said that "from the very beginning of the campaign, officials have shown signs of panic, probably because they don't like real opposition activists. Even if they didn't win, they could have taken a high number of votes. If that happened, it would have become clear how unpopular the current leader is."
Safanov said that a strong opposition vote would also have cast doubt on the results of a referendum in September in which residents of the region officially voted overwhelmingly in support of independence from Moldova.