Troicki had his suspension reduced from 18 months to 12 months by the Court of Arbitration for Sport on Tuesday after initially being handed the suspension by the International Tennis Federation.
The 27-year-old had refused to give a blood sample during the Monte Carlo Masters in April and will now be banned until 15 July 2014.
But Djokovic has defended his compatriot and was critical about the doping control officials after his win over Roger Federer at the ATP World Tour Finals.
“I think it’s just not bad news for him, it proves again that this system of Wada and anti-doping agency does not work,” said Djokovic, who has known Troicki since he was eight years old.
“I don’t have trust in them any more. I don’t have trust what’s going on.
“For me this is just another big reason, another example that there are some certain things that have to be changed.
“He’s going to be sanctioned until July next year, and this lady, the doping control officer, the representative that was there that day, she’s going to come back tomorrow for the job. Nobody is going to answer for that, only him. Why?
“The only one who is suffering here is the player. ATP, who is supposed to be an association of players of tennis professionals, who is supposed to be the governing body, the association that stands behind the players, are not going to answer on this announcement, are not going to do anything for Viktor.
“So Viktor is there by himself. Tomorrow can be anybody else. [Marin] Cilic was there in this situation.
“Tomorrow I don’t know who, just because of the negligence and unprofessionalism of these representatives, of so-called professionals.”