The 24-time Grand Slam champion agreed with Australian Nick Kyrgios, who on Saturday said integrity in the sport was "awful".
They were speaking in the wake of doping violations by world number ones Italian Jannik Sinner and Poland's Iga Swiatek during 2024.
The 37-year-old Djokovic, who will play doubles with Kyrgios at the Brisbane International this week, said there needed to be far greater transparency from the sport's governing bodies around doping violations.
And he said that it appeared that top players such as Sinner and Swiatek were being treated differently from those further down the rankings.
"I think Nick has some fair points when it comes to transparency and inconsistency with protocols and case-to-case comparables," the Serbian said.
"We have some players who have been waiting for over a year for their case to be resolved, so the issue is the inconsistency and the transparency."
While Djokovic said he believed Sinner when he said he tested positive to the steroid clostebol due to contamination from his physiotherapist, he asserted that the players had been "kept in the dark" throughout the whole process.
"I've been really frustrated, as have most of the other players, that we've been kept in the dark for five months," Djokovic said.
"He (Sinner) received the news (of the positive tests) in April and the announcement was not until August, just before the US Open.
"The ATP has not really talked in depth about why they kept that case away from the public.
"Then we had (Simona) Halep's case and Swiatek's case on the WTA Tour and it's not a good look for our sport."
'It's awful'
Sinner twice tested positive for clostebol in March.
However, the International Tennis Integrity Agency (ITIA) accepted his argument that the steroid entered his system due to contamination and opted not to suspend him.
The World Anti-Doping Agency (WADA) subsequently appealed the decision at the Court of Arbitration for Sport, with a verdict pending.
Swiatek tested positive for the heart medication trimetazidine (TMZ) in an out-of-competition sample in August when she was ranked number one.
As with Sinner, the ITIA accepted that Swiatek's violation was not intentional and she received only a one-month ban.
In contrast, Halep was handed a four-year ban by the ITIA in 2022 after testing positive for roxadustat.
She argued it was the result of a tainted supplement and successfully appealed to the Court of Arbitration for Sport, which reduced her suspension to nine months and she returned to the court in March.
"I'm just questioning the way the system works," said Djokovic.
"Why are certain players not treated the same as other players -- maybe there's some ranking reasons behind it, or maybe others have more financial backing behind them or stronger legal teams."
Kyrgios has been scathing about the ITIA decision involving Sinner.
"Tennis integrity right now, and everyone knows it, but no one wants to speak about it -- it's awful," the Australian said on Saturday, adding that said the sport's image was being tarnished.
"I just think that it's been handled horrifically in our sport," said Kyrgios.
