He said he would refuse to play the US Open if organisers made it compulsory for players to be vaccinated should a jab be developed.
He is far from alone when it comes to conspiracy theories in south-east Europe.
One poll suggests that three in 10 people share similar views.
Several countries suffered badly from a recent measles outbreak, with inoculation rates dangerously low.
Does this scepticism of mainstream science explain the resurgence of coronavirus in this troubled region?
In part, argues James Ker-Lindsay, visiting professor at the London School of Economics, the Djokovic episode "plays into something strongly felt in the region".
He added: "It's ingrained in the culture. But there are, of course, other reasons."
Initial hardline lockdowns were tough but successful, with death tolls a fraction of Italy, France, Spain, and the UK.
But Romania, Bulgaria, and Albania are now seeing record numbers of infections since the outbreak began, while other Balkan countries are recording daily infections akin to pre-lockdown highs.
They are sociable countries, and the easing of restrictions has seen a flurry of large wedding parties. Nightclubs are open. Big, intergenerational family meetings are common again.
Ker-Lindsay points to the legacy of Communist rule.
Early on, that meant the population was willing to accept a hardline lockdown. But there is now a suspicion some governments are using lockdowns as a cover to become more authoritarian.
Over the past week, Serbia has been rocked by nightly violent anti-government protests over a decision to reimpose a weekend curfew.
The authoritarian President Aleksander Vucic reversed that move, desperately trying to save face as he did so.
Ian Bancroft, a diplomat and author who lives in Belgrade, said: "Vucic was too quick to claim victory over the virus in Serbia. They were celebrating on the streets. It was too early."
Miran Pogacar, a 31-year-old activist in the northern city of Novi Sad, said: "Vucic ended the lockdown for the sole reason of organising elections."
Pogacar was detained by police for 40 hours last week. Dozens of protesters have been hurt.
Serbia went from a strict lockdown - which saw dog owners rent out their pets to give neighbours an excuse to get out of the house - to declaring total victory in mid May.
Vucic was desperate for parliamentary elections on June 21 to cement his grip on power.
Now Serbia is recording about 300 new infections a day and people are questioning the Government's handling of the crisis.
Zoran Sarac, 36, said: "People want to say goodbye to Vucic."
As Serbia's curfew plans were scrapped, Ana Brnabic, Serbia's Prime Minister, announced gatherings were to be limited to no more than 10 people. Still the protests continue.
Elsewhere, Albania recorded its highest number of infections - 117 yesterday. Bosnia and Herzegovina has seen big spikes in infections over the last two weeks, while Croatia and Montenegro are now back to recording pre-lockdown highs.
Bulgaria has reintroduced some restrictions after several consecutive days of record confirmed infections.
Romania's Constitutional Court last month ruled that the Government no longer had the power to enforce quarantine, isolation, or hospitalisation measures, declaring such moves a "deprivation of liberty".
That not only hits the country's weaponry to counter a resurgence, it led to hundreds of infected patients discharging themselves from hospitals.
According to an opinion poll by the Romanian Institute for Evaluation and Strategy, a third of Romanians would refuse a Covid-19 vaccination, should it be developed.
That is more than twice as many as in Britain, a YouGov survey suggests.
Claudiu Tufis, an associate professor of political science at the University of Bucharest, says: "There are a lot of Romanians who do not understand how science works or trust scientific arguments based on facts."
As if to underline the point, a debate last week in the Chamber of Deputies featured various civic groups - among them, those who deny even the very existence of Covid-19.
