Two people have been arrested over the shooting of a reporter last week, with police saying it was a revenge attack.
Witnesses say Jean Leonard Rugambage, the acting editor of Umuvugizi newspaper, was fired on by two men who then fled in a car.
The government has denied as "baseless" accusations it was behind the killing.
A police statement says one of the suspects is related to someone allegedly killed by Mr Rugambage during the 1994 genocide.
Mr Rugambage, who is survived by his wife and a child, was acquitted of genocide crimes by a local "gacaca" court in 2006.
Human rights groups have accused President Paul Kagame of intimidating the media and the opposition ahead of elections due to take place in August.
A police statement quoted by the pro-government New Times newspaper says the pistol used to shoot Mr Rugambage has been recovered.
The authorities recently suspended the Umuvugizi paper, prompting it to start publishing online instead.
Editor Jean Bosco Gasasira, who fled to Uganda in April after his paper was suspended, said Kigali had masterminded the assassination of Mr Rugambage who died in hospital after the shooting.
"I'm 100% sure it was the office of the national security services which shot him dead," he told US state-funded radio Voice of America.
Mr Gasasira said it was because of an article published on the Umuvugizi website relating to the attempted killing earlier this month of former army chief Lt Gen Faustin Kayumba Nyamwasa in South Africa.
But Foreign Minister Louise Mushikiwabo strongly denied such accusations.
"Of course, this is not true, it's baseless," she told the AFP news agency.
"We are not a government that assassinates journalists, we are a responsible government."
The government has also denied accusations it was behind the shooting of Lt Gen Nyamwasa.
He went into exile in South Africa earlier this year after falling out with President Kagame.
In April, Mr Kagame reshuffled the military leadership and two high-ranking officers were also suspended and put under house arrest.
Earlier in the month, Umuvugizi was suspended for six months by the press council for inciting opposition to the government.
Its website, launched in May, is not currently accessible through Rwandan internet providers; the authorities deny involvement in blocking it.
Mr Kagame's government argues that it must take care to control the media and politicians to avoid a repeat of the genocide, in which some 800,000 ethnic Tutsis and moderate Hutus were slaughtered.