The IOC officials were reportedly surprised at their hotel to be met by a court member seeking the president of the coordination commission for the 2016 Games, Nawal El Moutawakel, to sign the order notifying her and the IOC of the dispute.
The International Olympic Committee and 2016 Rio committee have downplayed the issue as golf prepares to make its return to the games for the first time in 110 years.
According to Sergio Antunes Lima Jr, the lawyer of the company which is claiming ownership of the area where the 2016 Rio committee says the golf course will be built, El Moutawakel and the other IOC members seemed confused when they were approached by the court official and there was a lot of discussion until lawyers from the 2016 Rio organising committee finally arrived.
Lima Jr, who said he was accompanying the court official, said Rio 2016 Organising Committee President Carlos Nuzman also arrived later.
The 2016 Rio committee, which last year went through the embarrassment of having to fire several employees who illegally downloaded files from British organisers during the 2012 London Games, said it was not involved in the court order and only gave support to the IOC officials as the document presented to them was in Portuguese and dealt with Brazilian law.
The IOC did not immediately answer a message for comment.
The court document named El Moutawakel and the IOC's coordination commission, as well as the local Public Olympic Authority.
"It was a notification just to show that they are still fighting for the land," Rio de Janeiro Mayor Eduardo Paes said. "Nothing changes right now."
There has been a long legal dispute over the land which is claimed by two different companies. Local organisers say they have enough guarantees from the businessman who says he is the current owner, but a judge has already said that any contracts made over the land will eventually be deemed illegal and nullified in case a court ruling goes against him.
Elmway Participacoes, which has challenged the ownership and claimed the land for several years, has already said it does not plan to build a golf course on the disputed land. Lima Jr said the goal was to build a commercial and housing complex in the area.
Construction of the course - which will host golf's first appearance at the Olympics since the 1904 St Louis Games - was expected to start in October, but the 2016 committee and local organisers recently said that the delay was not related to the legal case.
Paes said on Wednesday that the work will begin as soon as the needed environmental licenses are secured, which he expects to happen soon.
Local organisers have said there is no Plan B, and the International Golf Federation has reportedly expressed concern over the golf course - which will be designed by American Gil Hanse - because it wants it ready for test events in 2015.
The Rio committee is coming off major leadership changes and there is still no official budget available for the Games, putting local organisers under pressure to show that preparations for the first Olympics in South America are on track.
The IOC's coordination commission is making its first official visit of the year to Rio, and fourth since the city won the bid to host the Games in 2009. Its goal is to monitor the progress at venues and infrastructure sites.
The IOC said in December that "time is ticking" and organisers must attack the project "with all vigour."