Novak Djokovic, the top player in men’s tennis and its leading vaccine skeptic, was stopped at the border in Melbourne late Wednesday after flying from Dubai to defend his Australian Open title.

State government and Australian tennis officials had granted Mr. Djokovic an exemption from Covid vaccination rules that would allow him to compete in the event. But upon his arrival, federal border officials said that Mr. Djokovic did not meet the country’s requirements for entry because he was unvaccinated, and they canceled his visa. He filed a legal appeal on Thursday.

The exemption had stirred anger in Australia, which has enforced tough rules to prevent the spread of the coronavirus and has maintained one of the world’s lowest Covid death rates. Citizens who endured long lockdowns, and for months faced strict limits on leaving or returning to the country, demanded to know if Mr. Djokovic had been given special treatment.

Mr. Djokovic’s limbo appears to be rooted in confusion over the exemption granted by Australian tennis officials and local authorities in Victoria, the state where the tournament is held. The exemption was believed to have been approved because of Mr. Djokovic’s previous coronavirus infections — grounds that federal officials had warned were invalid.

Here’s a look at how the standoff has unfolded:

Djokovic has long provoked controversy with his views on science and medicine.

Mr. Djokovic has received scrutiny for his unscientific beliefs, including his assertion that positive emotions can purify toxic water or food. He has been dismissive toward the pandemic and said vaccinations should not be mandated for travel.

In June 2020, with tennis and other sports paused because of the coronavirus, he organized a charity tournament in his native Serbia and nearby Croatia. Masks and social distancing were minimal, and several players, including Mr. Djokovic, later tested positive for the coronavirus.

A surprise exemption gave him an apparent chance to defend his title.

Mr. Djokovic has won the last three Australian Opens, and nine overall. But his vaccine stance put in doubt his ability to defend his title.

Last year, the Australian Open said participants would have to be fully vaccinated, in line with requirements for entering the country. Mr. Djokovic’s participation was seen as unlikely until he announced on Tuesday that he would play after receiving an exemption.

He did not say why he had received the exemption; neither did Australian tennis officials. But they explained that 26 people who had applied for a vaccine waiver had had their requests reviewed by panels of medical officials from both Tennis Australia and the state of Victoria. A small number were granted.

The requests were reviewed under guidelines from an official government advisory body on vaccinations. The group listed several possible reasons for exemptions, including a Covid-19 infection within the last six months, inflammatory cardiac illness, or acute medical conditions such as major surgery.

Mr. Djokovic’s application was based on a recent infection, The Sydney Morning Herald reported.

The federal government steps in, stopping Djokovic at the border.

Mr. Djokovic’s exemption was denounced by many in Australia as the Omicron variant has driven a jump in new cases and residents have faced long delays in testing.

After Mr. Djokovic arrived in Melbourne, he was questioned for hours at the airport before being sent to a quarantine hotel. Prime Minister Scott Morrison of Australia, who has faced criticism over the government’s Covid response in recent days, announced that Mr. Djokovic’s entry had been denied.

“Rules are rules, especially when it comes to our borders,” Mr. Morrison wrote on Twitter. “No one is above these rules.”

In November, Greg Hunt, the Australian health minister, said in a letter to Craig Tiley, the head of Tennis Australia, that people who had contracted Covid-19 and had not been fully vaccinated would not qualify for quarantine-free entry.

Mr. Hunt added that the grounds for an exemption, such as a recent infection, are meant “for domestic purposes only — such as interstate travel, or meeting workplace vaccination requirements — and does not apply in the context of international borders.”

It was not clear why Tennis Australia and the Victoria government then granted Mr. Djokovic the exemption.

Mr. Morrison said on Thursday that there had “not necessarily” been any problem with Australia’s initial granting of a visa to Mr. Djokovic, and that it was up to travelers with visas to show proof of full vaccination at the border.

Djokovic lodges an appeal in the courts.

Mr. Djokovic filed an appeal in federal court in Victoria, and he will be allowed to remain in the country at least until Monday as he awaits a hearing. It was also unclear if quarantine remained an option, or whether Mr. Djokovic would accept it. The tournament starts in 11 days, sooner than Australia’s usual two-week quarantine.