The order came after Ezekiel refused to change articles that criticized police "for intimidation of innocents," he said.
The articles follow clashes this week that left 14 policemen and three civilians dead when citizens resisted attempts to relocate them from a crowded area of the capital to a camp for internally displaced people.
The newspaper reported eyewitnesses saying 33 people were killed and that police had fired into the crowd. The report did not include the government version of the story, which said no weapons were fired.
The United Nations called on the government and all concerned parties to "exert maximum restraint in handling the situation to prevent further escalation and loss of life."
Ezekiel said he was waiting to hear from police or other authorities about whether the paper was closed down.
"It is not a good step. The government ... continues harassing the media despite the signing of the peace agreement and the country's preparations for peace," Ezekiel said.
He said he would protest the halt in publication to the Press Council, human rights organizations and the United Nations.
The Monitor, an independent newspaper, has had its license suspended in the past for publishing articles critical of the government. The paper is particularly known for criticism of conditions in southern Sudan, scene of a 20-year civil war that ended early this year with the signing of a peace agreement between the government and southern rebels.
Sudan has a history of suspending newspapers and detaining journalists. The government has officially lifted state censorship of newspapers but press restrictions continue.
Earlier this month, the pro-Islamist Al Wifaq daily was indefinitely suspended for running articles considered blasphemous. Editor Mohamed Taha Mohamed Ahmed was arrested for violating a three-day suspension order and ignoring another ruling banning the media from writing about the case.