In one high-profile case, Faisal Mohammed Salih, a political columnist for a Khartoum newspaper, was summoned by intelligence agents every day for almost two weeks before they charged him, said the New York-based watchdog.
Salih, who is also a media consultant, had commented on international television about a speech made by president Omar al-Bashir at the height of tensions with South Sudan, HRW said.
Sudan and South Sudan fought along their border in March and April, creating fears of a wider war and leading the UN Security Council on 2 May to demand a cessation of hostilities and a resumption of talks.
"Sudan is blacklisting journalists and censoring articles on topics of great importance at this volatile time," said Daniel Bekele, Africa director at Human Rights Watch. "Sudan should immediately stop these tactics and show respect for basic freedoms."
HRW said intelligence agents this month censored an opinion article in the Al-Sahafa daily, and another in Al-Tayar which questioned the claim that Sudan was victorious at Heglig, the north's main oil field which South Sudan occupied for 10 days.
In April, security officials warned a journalist for the Al-Jarida daily not to write about the Heglig conflict, HRW said.
Another watchdog, London-based Amnesty International, this week called on Sudanese authorities to halt "ongoing harassment" of independent media.
"The authorities are deploying a wide array of coercive measures against individuals and media organisations to discourage or prevent independent reporting and critical comment," Jean-Baptiste Gallopin, Amnesty International's Sudan researcher, said in a statement. State intelligence agents ordered three newspapers shut earlier this year while others have had their print runs seized.
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