The 13 -- a male manager and 12 female employees of a Pyongyang-run restaurant -- arrived in Seoul last week, South Korea's Unification Ministry said.
Ministry spokesman Jeong Joon-Hee said they had been under pressure to meet their quota for hard currency remittances to Pyongyang and had become disillusioned with the North's propaganda after being exposed to foreign media.
The South Korean government estimates Pyongyang rakes in around USD 10 million every year from some 130 restaurants it operates -- with mostly North Korean staff -- in 12 countries, including neighbouring China.
"The manager, in connivance with (South Korean) spies, tricked the employees into believing that they were moving to a different workplace in a far-off place" before putting them on a plane, it said in a commentary.
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It said the "abduction" was part of the South's "heinous" anti-Pyongyang smear campaign.
South Korean daily Hankyoreh Sinmun quoted the Chinese owner of the restaurant in Ningbo, in eastern Zhejiang province, as saying the manager had stolen more than 1.2 million renminbi (USD 185,000) from the restaurant, which had a total of 20 North Korean employees.
The 13 defectors were still incommunicado, being questioned by South Korean authorities.
The North's Red Cross spokesman Tuesday claimed the 13 were kidnapped by the South and demanded it apologise and return them immediately or face "unimaginable consequences and strong countermeasures".
Separately, the North Korean website also accused Seoul of trying to influence South Korea's parliamentary elections held on Wednesday.
A seemingly unstable North Korea has traditionally worked in favour of the ruling conservative party.