The reason? Its editor Alfred Taban defied an order not to report on local government demands to be given more authority.
But Mr. Taban, whose career in the inky journalistic trenches of both Sudan and South Sudan has spanned decades – was not fazed.
"It didn't surprise me," he says, leaning back in his office chair next to towering stacks of papers lit by the glow of a computer screen. "I knew they would react negatively."
Having endured years of harsh censorship in Khartoum under successive dictators, Taban, from the south, hoped that independence for South Sudan would bring change.
But three years later, Taban says the press climate in Juba the capital is nearly as bad as his years in Khartoum, in Sudan.
Taban's story is similar to many South Sudanese who fought and labored for their country's freedom, only to feel let down by leaders now embroiled in a bitter and ugly civil war.
"They are doing the same things they were doing in Khartoum," he says of South Sudan's current rulers, whose disagreements in December brought a brutal war that remains unresolved.
Taban first moved to Khartoum in 1976 to attend university, then became the BBC's correspondent in 1981, and until 2007. But it was in 2000 when he began his most important and dangerous work, as he calls it – starting the Khartoum Monitor in order to report on the civil war for readers in the rebellious south.
"As a journalist in Khartoum they did everything," he says in a deep toned voice about the authorities. “Confiscation [of press runs] was like every week. We had our papers confiscated, articles that I write taken away … and I was detained so I don't speak out…."
Police in Khartoum twice closed his offices. There was little Taban could do, but he did not let the censorship go unnoticed.
When police pulled an article from the pages they asked for a replacement and Taban usually said there was none. When the newspaper appeared with blank spaces, readers knew there was censorship.
Sometimes Taban was harassed. While reporting on killings of Eritrean refugees fleeing into Sudan, security agents picked him up on a road notorious as a dumping spot for migrant or refugee bodies. For 40 miles of driving he wondered what his fate would be.
The most frightening episode came after reporting about low turnout at a pro-government rally. A security agent "well known for his cruelty," Taban says, arrested him in the morning and forced him to stare at the sun for hours.
Then agent made him sing, "I am a liar! I am a liar!" for 30 minutes. Taban did so without complaint. The agent, appearing frustrated, then took him to a "ghost house," an empty building used for torture and disappearances, and began hitting his stomach, meanwhile threatening to kill him.
Fortunately, he says, a security agent born in the south took pity and kept him safe.
Today Taban feels his reporting was part of the liberation struggle.
"Many southerners depended on journalists … to tell them what is really happening," he said. "Many of them did not really know what the [rebel movement] struggle was all about."
Taban’s tenacity earned him a 2006 meeting in the Oval Office with President George Bush where he received a National Endowment for Democracy award.
Even at the White House Taban pushed the envelope and disagreed with President Bush over a peace agreement between Khartoum and southern rebels.
"Whatever information you're getting, that peace agreement is not being implemented by the government in Khartoum," he told Mr. Bush as the BBC reported at the time.
On July 8, 2011, a day before South Sudan independence, Taban closed the Khartoum Monitor and moved south to start the Juba Monitor. He reduced staff and until May this year had to fly in the papers from Khartoum since South Sudan had no modern presses.
But Taban’s biggest problem is the ruling government's attitude about press freedom, especially given the civil war. He’s been detained four times since 2011. He and other editors receive calls from the government not to report on topics like corruption. The confiscation of the July 3 paper was the third such incident this year, and came a day after South Sudan's press minister pledged to uphold press freedom.
"This is really a disaster," he says. "The government is aware that people are starved of information...and this makes the government very nervous."
Two foreign correspondents have been arrested here and three kicked out of the country. Government minders shadow reporters at bars and during public events. Journalists complain of their phones being tapped. Anything security-related – which currently appears to constitute every moment and place -- is off limits for photography.
But sometimes Taban is surprised by the power of the press.
After implicating a government official in a murder last year, Taban found a police officer waiting in Juba's airport with an arrest warrant. But the officer turned out to be a family friend from his days in Khartoum. The man shook Taban’s hand and gave him a lift home, where the Juba Monitor offices are located in an attached building.
The editor has suffered ill health but still gets up at four each day to get a jump on the news, and he churns out two columns a day, six days a week. He doesn’t want to hear about retirement, saying there's work to do.
"[In Khartoum] I was supporting the rights of the marginalized people," he says. "Our struggle now is the issue of underdevelopment, because the money has been looted by the people in the government."
"They tried to kill me in Khartoum and they didn't succeed," he shrugs. "I will not keep quiet."