He was piloting a seaplane along with another man on Saturday when they landed on water. However, the heavy waves turned the plane over and swept it away.
Both men are understood to be German nationals. The other passenger managed to swim ashore while the search was carried out for the pilot.
"According to his own statement he had been swimming for about two hours. When he arrived on land in Visingsö he met with a local resident who helped him raise the alarm," Maria Ottosson of the Swedish Maritime Administration told the TT news agency.
Despite a heavy search involving boats and a helicopter throughout Saturday evening the missing German was not located. The plane was later recovered while the search mission ended at 11pm.
"We believe there is no longer any chance of finding someone alive," said Ottosson.
The search resumed on Sunday morning involving emergency services and the Jönköping police. Police will comb the area in boats and there will be also be dog patrols in operation on the shore.