Human Rights Watch said on Tuesday that Nhial Bol, former managing editor at the Khartoum Monitor, fled Sudan to Kenya in late October.
His decision followed repeated government actions against the Monitor, and arrests and threats against his life, said HRW.
The Monitor has been shut down several times this year by the government, most recently in September.
The only English-language daily in the country, the newspaper served Khartoum's large southern Sudanese population.
HRW said its articles on human rights abuses by security forces, slavery, and the treatment of southern Sudanese had aroused the ire of the Khartoum government.
Bol now intends to move to southern Sudan and start a newspaper in the territories of the rebel Sudan People's Liberation Movement/Army (SPLM/A).
"The international community needs to support Nhial Bol and other journalists like him so that they can continue to shine a light on human rights abuses"
Human Rights Watch
Jemera Rone, Human Rights Watch's Sudan researcher, said after the National Press Council instructed newspapers not to report on the peace process, there was a wave of crackdowns against the independent press.
Brutal civil war
She said: "An independent press will have a critical role to play in the future of Sudan, both in the south as well as the north
"The international community needs to support Nhial Bol and other journalists like him so that they can continue to shine a light on human rights abuses."
Sudan's brutal civil war has claimed more than one million lives over the last 20 years.
Ongoing peace negotiations to end the war between the SPLM/A and the government should be finalised by the end of the year.
Under the peace agreement, a regional government will be formed in the south, with the SPLM/A as the dominant party.