Muddy waters in the Yellow Sea, over which the rocket disintegrated on Friday, hampered the search of naval ships and helicopters, officials said.
The North said the rocket would launch a satellite, but critics saw it as a banned test of missile technology.
The UN on Monday strongly condemned the launch and ordered tighter sanctions.
At least 10 South Korean warships have been combing the waters where the Unha-3 rocket fell after exploding, 165km (105 miles) west of the South Korean capital, Seoul.
“No debris has been found and the operation will end officially at 17:00 (08:00 GMT),” a defence ministry spokesman was quoted by AFP news agency as saying.
Vessels from China, Russia and the US have also been searching for rocket debris, South Korean officials have said. Experts say the debris could offer an insight into the technology used by the North.
The North had warned before the launch that any attempts by other nations to retrieve any debris would result in “ruthless” retaliation.