The soldier dashed across the border at the Panmunjom truce village on Monday, as former comrades from the North opened fire on him, hitting him at least four times.
He was pulled to safety by three South Korean soldiers who crawled to reach him, just south of the dividing line.
The young man was rushed to hospital in South Korea by helicopter where he has undergone two rounds of emergency surgery.
"Vital signs including his pulse are returning to stability", attending doctor Lee Cook-Jong told journalists.
However, he warned, the un-named soldier could rapidly deteriorate at any moment.
"We're paying close attention to prevent possible complications," said Lee, who on Wednesday said "an enormous number of parasites" including roundworms had been found in the small intestine.
"I've never seen anything like this in my 20 years as a physician", he said, adding the longest worm he removed was 27 centimetres (11 inches).
Parasites, especially roundworms, are widespread in North Korea -- as they are in many developing countries -- where people eat uncooked vegetables that have been fertilised with human faeces, experts say.
They were also common in South Korea until the 1980s when the country was wealthier and the use of commercial fertilisers became widespread.
"The contamination... was very severe, and the future course of his medical condition is likely to be worse than that of general trauma patients as he was in a state of shock for a long while due to massive bleeding," he said.
South Korean officials have said that troops from the North fired at least 40 rounds.
One of the worst wounds was in the man's abdomen, where the bullet shattered his pelvis.
It is very rare for troops to defect at Panmunjom, a major tourist attraction and the only part of the border where forces from the two sides come face-to-face.
Unlike the rest of the frontier, the village is not fortified with minefields and barbed wire, with the demarcation line marked only by a low concrete divider.
North Korean sentry guards at Panmunjom are all carefully screened and vetted before being deployed there.
No personal details have been released but the soldier's uniform suggested he was low-ranking.
The US-led United Nations Command (UNC), which monitors Panmunjom, said the soldier had driven close to the military demarcation line separating the two Koreas.
He then dashed from the vehicle and ran towards the border as other North Korean soldiers opened fire.
South Korean troops did not return fire.
Dozens of North Korean soldiers have fled to the South through the heavily-fortified border over the decades since the peninsula was divided, including two soldiers who crossed the frontier in June.
More than 30,000 North Korean civilians have also fled their homeland since the two nations came into being in 1948, but it is rare for them to cross the closely guarded border.
(Except for the headline, this story has not been edited by NDTV staff and is published from a syndicated feed.)
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