Ntwali, 44, editor of The Chronicles newspaper was killed on Wednesday when a speeding vehicle rammed a motorcycle he was riding on.
Police says the accident occurred at 2:50 am on Wednesday.
Speaking to VOA’s Eric Bagiruwubusa in the capital Kigali, traffic police spokesperson Senior Superintendent Irené Irere, said a motorbike on which Ntwali was riding was hit by a car killing him on the spot and injuring the person who was riding with him.
Ntwali who has been arrested multiple times during his two-decade career as a journalist, owned the channel Pax TV on YouTube which had established itself as a rare outlet for critical reporting in Rwanda.
The driver involved in the accident is in police custody, the officers told the local media.
"Ntwali didn't have any identification on him," the officers said, adding that he was identified on Thursday.
"We immediately informed his relatives."
A family member who sought anonymity owing to the sensitivity of the case said they were shocked by the death.
"I last saw him on Tuesday afternoon, and we spoke on phone again that night. I did not hear from him again," they said.
“He looked cautious and switched off his phone before we started talking. He said phones could not be trusted. He told me that all the doors on which he knocked were closed but he was determined to face life. His death was so sudden" said Bihibindi Nuhu, a journalist.
They met the evening before he died to discuss the state of independent media in Rwanda.
Ntwali’s death, which was not known until Thursday afternoon, has come as a shock to a number of people, including journalists and politicians especially those who were critical of the Rwanda government.
Some of them expressed skepticism and said they want more than just an ordinary investigation into his death.
Victoire Ingabire, a Rwandan politician and founder of the yet to be legally approved DALFA- Umurinzi political party, says she was shocked by the news. Ingabire told VOA that she had scheduled an interview with Ntwali on Wednesday.
However, every time she sent him a message, she noticed that the messages remained unread until Thursday after his death. She said whoever read her messages afterwards did not reply.
“It would be good if the circumstances surrounding his death were clear. Because it is unclear saying that a well-known person like Ntwali died in an accident and two days go by before people know about it. It would be good for those in charge to explain it to avoid rumors”, she said.
Media is tightly controlled in Rwanda and journalists critical of President Paul Kagame and his ruling party have been jailed, have disappeared or turned up dead throughout his nearly 30 years in power.
The country's media played a central role in whipping up racial hatred in the lead up to the 1994 genocide that saw 800,000 mainly ethnic Tutsis killed in a 100-day massacre.
Reporters Without Borders (RSF), a media watchdog, says Kagame "exploits Rwanda's collective memory" of the genocide to justify his control over the media.
The media landscape in Rwanda "is one of the poorest in Africa", with journalists harassed, surveilled and prosecuted for their work, RSF says.
"Since 1996, eight journalists have been killed or reported missing, and 35 have fled abroad," RSF says on its website.
Anjan Sundaram, who lived in Rwanda and wrote about the shrinking space for media in his book "Bad News: Last Journalists in a Dictatorship", said Ntwali was a target.
"He was on a hitlist of Rwandan reporters critical of the government," Sundaram wrote on Twitter.
Human Rights Watch called on Friday for a "prompt, effective investigation" into the death, saying that Ntwali "joins a long list of people who have challenged the government and died in suspicious circumstances".
On January 7, Ntwali reported on his YouTube channel that two teachers had gone missing for over a year after they were taken for questioning by intelligence officers.
Last year, he was a rare public voice of opposition to Britain's controversial plan to send migrants and asylum-seekers to Rwanda, describing it as "an immoral deal" that violated human rights.
This report was compiled with data sourced from Agence France Presse, and from VOA's Eric Bagiruwubusa and Geoffrey Mutagoma.