Kabuidibuidi, 41, is an outspoken critic of the regime in the Democratic Republic of Congo and came to Sweden in 2003 to seek political asylum.
However, the Swedish Migration Board (Migrationsverket) denied his request, ruling that Kabuidibuidi's life would not be at risk should he return to Congo.
After being held for the past four months at an immigrant detention centre outside of Stockholm and managing to avoid deportation on three separate occasions, Kabuidibuidi was whisked away by police and deported in secrecy on the night of Friday, February 24th.
The pastor's representative in Sweden, Claes Strömvall, was not even told of the move, and called the deportation "deplorable".
"The police wouldn't give me any information yesterday and cited security concerns," Strömvall said in a statement on Friday.
At first, Kabuidibuidi's supporters weren't even sure he had been deported, only receiving confirmation the following day from a cryptic SMS sent by the pastor to a supporter in Sweden.
"He is such a strong critic of the Congolese regime, and Congo is a dictatorship of divine grace. Everyone knows how they treat people there except the Swedish Migration Board," Strömvall told Expressen newspaper.
"We have argued that he could be imprisoned, tortured or executed. Now all of these have been done except the execution."
Kabuidibuidi was allegedly taken away upon arrival, before being beaten and then set free. He is now believed to be recovering in hospital.
"I have been tortured. They took all my money and my clothes. I am damaged and have pain all over my body. Now I am in hospital," he wrote in a text message to Expressen.
According to the Migration Board's rules, asylum seekers are usually allowed to stay in Sweden if there is a risk of them being tortured.
However, the agency concluded that, based on available information, there was little chance that Kabuidibuidi would be tortured when he returned to Congo, according to Expressen.
But the pastor's supporters in Sweden continue to contest the decision, especially in light of Kabuidibuidi's claims that he has been tortured.
"The pictures of the injured Pastor Jean show, in all probability, he has been subjected to torture and that the Migration Board has been wrong in their contention that they are no risks for Jean to be deported to the Congo," Maria Furusand, a pastor of Elimkyrkan in Stockholm, said in a statement.
"The Swedish government has put Jean's life at risk. Now, the rules must be revised so that no more people will be deported from Sweden to be tortured."
The Migration Board, meanwhile, stands by its decision.
"Our decision is based on the information we had access to," spokesperson Johan Rahm told Expressen.
Rahm also emphasized that it remains unclear whether or not Kabuidibuidi was actually tortured.
"I don't think you can draw that conclusion. The information that has come to light is unconfirmed," he said.
"With Yoweri Museveni and Dr. Kiiza Besigye Uganda is in anarchy"
Kuungana Mulindwa Mawasiliano Kikundi
"Pamoja na Yoweri Museveni na Dk. Kiiza Besigye Uganda ni katika machafuko"
"Nous ne nous souviendrons pas des paroles de nos enemis mais plutot du silence de nos amis"
"Tout militaire sans formation ideologique, c'est un criminel en puissance et malheur a ceux qui baillonnent leur peuple: Thomas Sankara"