The North had demanded the repatriation of all 31 of its citizens on the boat, which strayed into southern waters early last month. Seoul said four wanted to stay in the South.
South Korea's Red Cross said in a statement that the 27 people were handed over to North Korea's navy near the western sea border Sunday.
South Korea accepts North Koreans who choose to defect. More than 20,000 have done so since the Korean War ended with an armistice, not a peace treaty, in 1953. Six arrived by boat last week and sought asylum.