"There was a problem in the automatic launch sequence that caused the launch to be called off," Lee Joo-Jin, who heads the Korea Aerospace Research Institute, said.
The $400m Korea Space Launch Vehicle-1 (KSLV-1), or Naro-1, had been scheduled to be launched from the Naro Space Centre at Goheung off the southern coast at 5pm local time (08:00 GMT).
But it was halted less than eight minutes before lift-off.
Mission controllers suspended the launch, reattached Naro-1 to the launch pad and began dumping the rocket's fuel, the South Korean science ministry said.
It is the seventh time since 2002 that the project, operated in partnership with Russia, has been delayed.
If South Korea does complete a successful launch, it will become the latest nation to join the region's space race and the 10th in the world to send its own communications satellite into orbit from its own soil.
But any space launch is expected to rile North Korea, which was severely censured four months ago for launching a long-range rocket widely seen as a disguised missile test that violated UN sanctions.
Seoul has bristled at any comparisons with the North's operation, insisting its launch is purely for scientific purposes.
"North Korea is not happy with South Korea acquiring advanced space rocket technology," Baek Seung-joo of the Korea Institute for Defence Analyses told the AFP news agency.
The North condemned the UN for punishing it with further sanctions over the launch of what it says was a peaceful communications satellite into orbit in April.
|The KSLV-1 rocket was made with the help of Russian technology [EPA]
It expelled inspectors and pulled out of six-party talks on its nuclear programme in response.
Ralph Cossa, president of the Hawaii-based Pacific Forum at the Centre for Strategic and International Studies, told Al Jazeera that North Korea lost the right to launch satellites two years ago when it began a series of missile tests that violated the terms of UN sanctions.
"The North Koreans keep shouting about double standards but the point is they earned that double standard by what they did in 2006 and then with the nuclear test earlier this year," he said.
A North Korean foreign ministry spokesman earlier this month said Pyongyang would be closely watching the UN's reaction to South Korea's launch.
The US dismissed North Korea's complaints on Tuesday, saying that Seoul's space programme was transparent and responsible, the South Korean Yonhap news agency said.
South Korea has already sent 10 satellites into space using launch vehicles from other countries. Its first astronaut entered space on board a Russian Soyuz rocket in April last year.
The South's two-stage rocket is supposed to launch into orbit a 100kg satellite that will monitor the Earth's radiant energy which includes observing the atmosphere and ocean.
South Korea aims to build a rocket completely on its own by 2018 and send a probe to orbit the moon by 2025.
It also wants to develop a commercial service to launch satellites.