South Korea's defence ministry website was among those that remained down for a third day and access to some US government sites, including the State and Defence Department, from South Korea appeared to have been disabled.
Park Chul-soon, an official with South Korea's Communications Commission said the impact could spread as more people go online through the day.
"We've had the first wave and the second wave, and now there may be a third one," he said on local radio.
|No one has claimed responsibility for the cyber attacks in South Korea [GALLO/GETTY]
Some analysts however have raised doubts that North Korea may have been behind the attack, saying the implications of state involvement were severe, and that it may instead be the work of industrial spies or pranksters.
If the North was responsible, it would mark add a new dimension to an already tense stand-off between the two Koreas following Pyongyang's nuclear test in May, and the launching of ballistic missiles in June and July.
Mark Rasch, a former US Department of Justice official on cyber crimes, told Reuters news agency that the implications of a state-sponsored attack were severe.
"There's no difference between dropping a logic bomb and dropping a TNT bomb in the law of war," he said.
He also said that while North Korea could have been behind the manoeuvres, they did not appear to be coming from computers physically based there.
"The DPRK [North Korea] is fully ready for any form of high-tech war"
June 27 commentary on KCNA, official North Korean news agency
The South Korean and US shutdowns resulted from what is known as a "denial of service" attack, in which web servers are swamped with thousands of simultaneous requests, forcing them to shut down.
South Korean officials have said the attacks appeared aimed only at paralysing the sites, rather than penetrating secure networks or stealing sensitive information.
No clear evidence has yet come to light as to who may be behind the South Korean attack, but it comes just weeks after South Korea's military announced it was setting up a special cyber warfare command to fend off attacks from the North and other countries.
According to a report released in May, South Korea's military networks experience an average of tens of thousands of hacking and virus attacks every day.
N Korean warning
Last month, the North warned of "high-tech war" against the South for spreading what it said was false information about its involvement in cyber attacks.
"As universally recognised, the US is the kingpin of 'cyber attack' and 'hacker intrusion' on our planet," its official KCNA news agency said on June 27.
"The DPRK [Democratic People's Republic of Korea] is fully ready for any form of high-tech war," it said.
The incident however, is not peculiar to the Korean peninsula.
Last year, in the weeks leading up to the war between Russia and Georgia, Georgian government and corporate websites began to experience a sudden string of "denial of service" attacks.
Russian government officials denied involvement, but after investigating domain names and website registration data, a group of independent Western computer experts concluded that the Russian security and military intelligence agencies were involved.