Lee Myung-bak had pledged to pursue a hardline policy toward the North and hold it accountable for its nuclear disarmament promises.
North Korea acknowledged for the first time last week that H1N1 flu had broken out in the country, after Seoul offered unconditional aid to help contain the spread of the virus.
The North did not mention any virus-related deaths, but a Seoul-based civic group claimed that the disease had killed about 50 people in the North since early November.
Kim Young Il, the chief of humanitarian support at the ministry, said his government decided to provide H1N1 medicine in a " humanitarian manner".
The delivery was a sign that South Korean government cared about the North Korean people's well-being, he said.
The aid, accompanied by South Korean doctors, was loaded onto refrigerated trucks in Dorasan and transported across the border to Kaesong city in North Korea.
'Act of crime'
North's Korean Central News Agency (KCNA) on Thursday cited an unidentified source as saying that the South Korean military staged underwater explosive exercises around the border - the scene of a naval clash last month that left one North Korean sailor dead and three others wounded.
The drills represented "a threat and an unpardonable act of crime against us," KCNA said.
South Korea said the drills were routine and took place in the South's waters.
The North does not recognise the sea boundary between itself and the South, drawn by the United Nations at the end of the 1950-53 Korean War, and has long claimed that it should be redrawn farther south.
The dispute led to deadly skirmishes in 1999, 2002 and last month.
Relations between the two Koreas soured badly after Lee halted unconditional aid to the North in line with his pledge to get tough on his communist neighbour over its nuclear weapons development.