After landing in Dubai on Thursday, Rusabagi went to a hotel, the official said, five hours before taking off from Al Maktoum Airport after midnight.
“Mr Paul came and went legally,” a UAE official told CNN.
A longtime critic of President Paul Kagame’s rule, his travel immediately raises questions as to why he came on the jet knowing he would face charges on the plane.
In the days following his departure from Dubai, rights The 66-year-old human rights activist was confronted in Rwanda, facing charges related to terror in a handcuffed parade.
Rwanda Investigation Bureau (RIB) spokeswoman Thiri Murangira, speaking from Kigali, would not elaborate on how and where Rusabagina was arrested, saying “serious crime charges” would have to be answered.
He said the arrests were made in co-operation with the international community.
However, a UAE official has confirmed that there is no agreement between the Gulf state and Rwanda for the extradition of criminals or wanted persons.
They said Rusabagini had visited Dubai twice in the last few years and had not expressed any suspicion from officials in the UAE, as he was not on any wanted list.
The RIB did not respond to questions about the apparent difference.
Fear of family kidnapping
Rusabagina’s family told CNN they believe she was abducted, but there is no evidence of this.
New information from the UAE deepens the mystery of his arrest and raises new questions about claims made by Rwandan authorities.
The official said Rousseau, who had traveled by himself, arrived in Dubai on a Emirates flight from Chicago last Thursday evening.
At the same time Rusabagina checked in with his wife and daughter by phone, the family told CNN.
“This is the last time we’ve talked to him, this is the last time we’ve heard from him and he’s been silent ever since,” said his son, Tracer Rusebagina.
He said he was surprised that his father also ventured into the UAE.
Although her father traveled extensively, she had recently cut off her travels due to the epidemic, and the family had long feared the strong intelligence network of the Rwandan government.
“I was shocked to hear he was in Dubai, that he was anywhere near Africa,” he said.
They claim that Rwandan agents have been following Paul Rusabagina regularly for over a decade, raiding his home and threatening his life.
Her family is also concerned about her health as she is a cancer survivor and a heart patient who needs medication every day.
They have not contacted him since his disappearance and have requested to visit him immediately.
The RIB and Rwandan leadership figures had earlier said that the allegations facing Rusabagina were not related to politics.
The RIB says it is accused of supporting terrorist groups, calling for violence and engaging in specific acts of terrorism.
Pressed on that clarity, RIB spokesperson Murangira told CNN on Tuesday that the investigation is around alleged crimes against civilians in two districts of Rwandan in June and December, 2018.
Murangira said investigators have 15 days to decide whether Rusibagina should remain in custody, whether she has the right to speak to a lawyer and her family.
About 800,000 Tutsi and moderate Hutus were killed in the Ruwandan genocide, led by Hutu extremists.
Opposing voices fell silent
His family and foundation say Rousseau has Belgian citizenship and U.S. citizenship. There is also a green card. A U.S. State Department official told CNN he was aware of his arrest and was monitoring the situation.
He has not lived in Rwanda since 1996, when he survived an assassination attempt.
While Rwanda was widely praised for its transformation after the genocide, Kagame also faced widespread criticism for violating human rights and silencing dissent.
Opposition politicians in Rwanda have often jailed themselves for allegedly standing against Kagame in the polls.
In more widely publicized cases, Diane Rvigara and her mother were jailed while previous people tried to run for president in the same election as Kagame in 2017.
FDU-Inkingi Party leader Victor Ingabair was jailed in 2010 on charges including terrorism, “separatism”, “genocide reduction” and “genocide ideology”.
She returned from the Netherlands to run in the 2010 presidential election after years abroad, but was barred from running, and was sentenced to eight years in prison before being pardoned in 2018.
CNN’s Stephanie Busari and Eon Muskuni contributed to the report.
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