Malek Jaziri had been scheduled to play Israel's Amir Weintraub on Friday in the quarterfinals of an ATP Challenger tournament in Tashkent. He withdrew before the match and Weintraub advanced to the semifinals of the lower-tier event.
"Following a meeting this afternoon with the Ministry of Youth and Sports, I have the immense regret to inform you that you are ordered not to play against the Israeli player," the federation said in an email to Jaziri.
The email was provided to Tunisia's state news agency by Jaziri's brother, Amir.
Sports ministry spokesman Sadok Touati confirmed to The Associated Press that the federation sent the email after consulting the ministry.
"The ministry does not interfere in the affairs of the sports federations," he said.
The federation president could not be reached for comment.
In an interview with a local radio station, Amir Jaziri said he and his brother were afraid the decision could impact the player's career. He is currently ranked 169th in the world.
Arab countries have for the past decades observed to varying degrees boycotts against Israeli athletes in protest over the situation of the Palestinians.
Shlomo Glickstein, director of Israel's tennis association, said in a statement it was sad such incidents still occur.
"It's a pity for the athletes who get caught up in these situations that end up hurting their personal career," he said.
The International Tennis Federation at the ATP said they were looking into the incident.
"We're aware of the story and have been in touch with the ITF today," ATP spokesman Simon Higson said. "There's a clear distinction between the ATP's jurisdiction over players and the ITF's over federations. We are looking into the specific circumstances of the case together with the ITF and will act accordingly."
ITF spokesman Nick Imison said the ITF would write to the Tunisian federation this weekend to learn about the circumstances.
"The ITF believes that sport fosters good collaboration between nations and as such players should be able to compete freely on the international circuit," Imison said. "If a federation were responsible for a player not taking part that would go against the ethos of the organization and against the ITF constitution."
He said the case was unprecedented in tennis and it was unclear what, if any, sanctions could be imposed.
"The most important thing going forward is for Tunisian players to be able to play freely against any opponents in the future," Imison said. "That is the aim of all the tennis governing bodies."
Associated Press writers Ian Deitch in Jerusalem and Tom Allnutt in London contributed to this report..