A total of 13 South Koreans are staying in the nation ridden with unstable security conditions.
The government has strongly requested that they depart the country for security reasons.
A South Korean man remains held hostage by an unidentified armed group there after he was kidnapped in July.
"(We) have taken the step of nullifying the passports of three (of the South Koreans), as they have refused to get out of Libya," the foreign ministry official told reporters on the condition of anonymity.
The government is trying to persuade the others to follow its advisory, he added.
Meanwhile, he confirmed that South Korea will begin a deep-sea search for the ill-fated Stellar Daisy bulk carrier in the coming weeks, nearly two years after it sank off Uruguay.
The work is to begin in late January or early February, and the final result is expected to come out before the end of March, he said.
The ship sank in the South Atlantic, some 3,700 kilometers off Uruguay, on March 31 last year. Eight South Korean and 14 Filipino crew members remain missing.
The government signed a contract with Ocean Infinity, a Texas-based seabed exploration firm, for the search. The deal, made through the Public Procurement Service, is worth 4.84 billion won (US$4.35 million).