Sudan's constitution enshrines press freedom but an unpopular national security law and other legislation allows authorities broad powers to restrict the press. The oil-producer held elections a month ago, marred by an opposition boycott.
The Ajras al-Huriya paper, allied to south Sudan's main party the Sudan People's Liberation Movement (SPLM) who signed a 2005 north-south peace deal, said half its content was removed by censors from the intelligence services.
"We cannot have an issue tomorrow because they removed six pages and the paper is 12 pages long," said acting editor-in- chief Fayez al-Silaik.
The paper says it is also facing five court cases raised by the intelligence services, the army and the police.
The independent al-Sahafa paper said it was also targeted on Wednesday night. Its editor-in-chief al-Nur Ahmed al-Nur told Reuters three full pages were removed as well as other articles.
"I don't see any reason for this," he said. "We are an independent and objective paper and we expect to be dealt with in an objective manner."
Sudan's intelligence were not immediately available to comment. In a midnight raid, the opposition al-Rai al-Shaab paper was closed down on Saturday, three senior editors arrested and their assets seized.
The paper is the mouthpiece of opposition Islamist leader Hassan al-Turabi who was also arrested and is being kept in solitary confinement, although his Popular Congress Party said none of them had been charged.
Rights groups condemned the move, which Khartoum said was a matter of national security.
Direct censorship of Sudan's mostly lively print press was removed last year ahead of April elections which returned President Hassan al-Bashir and his ruling National Congress Party with a large majority in parliament.
Opposition parties cried widespread fraud, which the NCP denied. The vote was undermined by opposition boycotts.
Al-Nur called the censorship a "step backwards in the democratic transformation of the country". Al-Silaik said it was the biggest crisis to face Sudan's press since a 2005 north-south peace deal ended decades of civil war, shared power and wealth and outlined a plan for democratic change in Africa's largest country.
Sudan's south will vote in less than eight months in a referendum on secession from the north which they have fought on and off since 1955 over issues including ideology, religion, oil and ethnicity.
The war claimed some 2 million lives and destabilized much of east Africa.
