Some were shot as they tried to flee. Others had their throats slit before their bodies were strung up from door frames. Two children were run down by a car.

These are the testimonies from South Sudanese refugees as hundreds fled into Uganda for a second day on Wednesday following an attack by government forces on the border town of Pajok.

At least 17 people were killed, according to a Reuters news agency tally, while roughly 3,000 refugees crossed into Uganda this week.

Their stories offer a glimpse of the brutality of a three-year civil war ripping apart the world's youngest nation.

Password Okot, 30, a farmer, recounted how he lost two brothers.

Having fled the initial fighting, he crept back to his home in Ywayaa village on Pajok's outskirts to collect his belongings. There he saw government soldiers grab his brother, 35-year-old mechanic Ayela Peter, from a crowd, tie his ankles, slit his throat and sling up his body in a doorway.

"When they saw them slaughtering my brother, people scattered and started running. When they were running, they shot my other brother," Okot said at the Ngoromoro border crossing.

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The government denies its Sudan People's Liberation Army (SPLA) forces target civilians and said Monday's operation in Pajok, a town of more than 10,000 people 15km north of the Ugandan border, was to flush out rebels.

A military spokesman blamed "bandits" for killing civilians.

SPLA deputy spokesman Colonel Santo Domic Chol said his troops had orders to refrain from entering and taking over Pajok. "What I know is that the bandits are looting and killing the population in Pajok, starting on Friday, Saturday."

South Sudan, which split away from Sudan in 2011 after decades of conflict, has been mired in civil war since President Salva Kiir sacked his vice president Riek Machar in 2013. Thousands have been killed as the civil war rages into its third year and more than 1.5 million people have fled the country in the past nine months alone.

The United Nations said in December it had evidence of ethnic cleansing by both government forces and rebels, with soldiers showing callous disregard for civilian life.

The Pajok assault is the latest in a string of attacks in the fertile Equatoria region that is emptying towns and villages near the border with Uganda and Democratic Republic of Congo.

Two refugees spoke of the SPLA troops overrunning Pajok's hospital and killing a medical worker.

Omal Koloro, 52, a businessman, said the doctor had tried to prevent SPLA soldiers from entering the compound. Four others at the hospital were also killed, Koloro said.

In another incident, he said children were targeted as they ran across a bridge at the first outbreak of gunfire. "Two were run over and two they just shot," he said.

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The Ugandan government and United Nations refugee agency (UNHCR) are scrambling to complete a half-built refugee settlement near Ngomoromo for the latest arrivals, who are living in the bush at the Ugandan border.

"We're trying to work out the best place for them to be accommodated," UNHCR spokesman Alvin Gonzaga said. "We're trying to ready the site but we need the signature of the landowners."

Even when they reach the relative safety of a settlement camp, many refugees face an agonising wait for loved ones who went missing in the panic two days ago.

The phone signal to Pajok has been cut.

"My mother is still there," Okot said. "We don't know whether she's alive or dead."