The gruesome practice came to light Sunday when Korea Customs said it had uncovered 35 attempts to import a total of 17,451 such capsules since last August.
The pills -- filled with the dried and powdered flesh of foetuses or dead infants -- were intercepted in the mail or in customs searches at airports.
The customs service said that apart from ethical questions the capsules were contaminated with "super bacteria" and other disease-causing organisms.
Most pills were sent from the northeastern Chinese cities of Yanji and Jilin as well as cities including Qingdao and Tianjin at the request of customers in South Korea, it said.
Some were hidden in packages of legitimate drugs to disguise their contents.
Officials now closely monitor flights from "certain Chinese regions" and inspect all the luggage of all passengers far more often than before, Kim Soo-Yeon, a Korea Customs official in charge of customs clearance told AFP.
Bringing in such pills breaches a regulation banning items that "violate social dignity and customs", he said.
No organised attempts to smuggle in the capsules have so far been detected, Kim said, and most offenders were individual travellers. Some claimed they were unaware of what they were carrying.
"It's not just human-flesh pills. We also target other similarly banned but popular items like seal penises and bear gall bladders," said Kim, referring to items favoured by middle-aged men as libido enhancers.
"We have drastically stepped up resources in these efforts...even risking great inconvenience to visitors from these regions," he said.
Chosun Ilbo newspaper said the human-flesh capsules sell for 40,000-50,000 won ($35-44) each at some oriental herbal medicine shops.
Experts say the practice stems from a superstitious belief that eating body parts of young infants will give one special physical strength or cure disease.
"It is a bizarre...practice, just like a belief that eating the penis of actively-mating seals or drinking the bile of strong bears will help your libido," Ha Ji-Hyun, a psychiatrist at Konkuk University medical centre, told Chosun.
Maeil Business Newspaper urged the Chinese government Tuesday to crack down on producers of the human-flesh capsules and impose heavy punishments, calling the practice "truly shocking."
"No government in the world could possibly understand the Chinese government for letting such an inhuman practice go unpunished," it said in an editorial.
It added that desperate cancer patients and construction workers from China undertaking gruelling work were the main customers in the South.
"I'm trembling with shock that people who eat such stuff are my compatriots," one anonymous South Korean Internet user commented. Another called the practice "absolutely hideous".