The rare attack took place in the early hours of Tuesday in the Yumbe district of Uganda's northern West Nile region, which lies close to the porous border with South Sudan.
"Police received the information that 20 civilians were abducted by suspected militia members from South Sudan," local police chief Ignatius Otong told AFP.
He did not say why a South Sudan group was suspected, but said Uganda security forces were working with their counterparts across the border.
Civil war erupted in South Sudan in December 2013 but rebel chief Riek Machar returned to the capital last month as part of a peace deal which saw him becoming vice-president and forging a unity government with President Salva Kiir.
However, fighting continues among multiple militia forces who now pay no heed to either Kiir or Machar.