"The problem is censorship. The government is trying to censor us, and we are fighting," William Ezekiel, KM's editor-in-chief, told IRIN on Sunday.
Ezekiel had received a call from security at 2300 GMT and was asked to replace two articles, both of which referred to the clashes that took place between internally displaced persons (IDPs) and Sudanese security forces in Soba Eradi IDP camp on Wednesday.
The fighting erupted when security officers tried to forcibly relocate IDPs from Soba Eradi, 30 km south of Khartoum. At least 30 people - 14 policemen and more than 20 IDPs - were reportedly killed.
One of the articles the paper was asked to remove referred to security forces and was entitled, "Stop Intimidating the Innocent". The second article expressed the distress of an IDP mother who had lost her 13-year-old daughter on Wednesday.
When Ezekiel refused to comply, security forces ordered that the printing of the Saturday edition be stopped.
Alfred Taban, chairman of the Khartoum Monitor's board of directors, told IRIN that the newspaper had been asked several times by security forces to replace articles that did not reflect the opinions of the government, but that this was the first time KM had refused to comply.
"We could have found a replacement, but we don't want the government to take away our rights," Taban told IRIN.
The KM was able to resume its regular business on Sunday, but Ezekiel told IRIN that the journal would continue to fight against censorship if it did not agree with the reasoning given by security forces to have an article removed.
"We need a more open society," Taban explained. "This is against the Comprehensive Peace Agreement [CPA, signed between the government of Sudan and the southern Sudan People’s Liberation Movement/Army on 9 January]. It says clearly in the CPA that there is freedom of the press! Is this freedom? How is forcing us to remove our articles freedom?"
The media watchdog, Reporters Without Borders (RSF), condemned the incident.
"The signing of peace accords in Sudan must not be allowed to mask what is a very difficult situation for journalists in Khartoum, where the state security police monitor and censor the privately-owned news media," RSF said in a statement on Monday.
"If the Sudanese authorities want people to believe in their declared desire to restore peace and build a democracy, they must start by respecting their own laws and the treaties they have signed and that means they must stop sending the police to newspapers," it added.