The launch prompted an emergency warning in Japan just before 4am local time over the J-alert broadcasting system, telling residents of the southernmost prefecture of Okinawa to take cover indoors.
About 20 minutes following the alert, the Japanese government followed up with a notice that the missile had passed through towards the Pacific Ocean and lifted the emergency warning.
Japanese Chief Cabinet Secretary Hirokazu Matsuno called the launch a threat to regional security and said officials would lodge a protest with North Korea.
A US official, speaking on condition of anonymity, confirmed the US military was aware of the North Korean launch but declined to offer details.
Two days ago North Korea said it would launch a satellite between August 24-31.
Officials in Pyongyang have said North Korea needs a military reconnaissance satellite to boost monitoring of US military activities.
But the North's May 31 bid to launch a Chollima-1 satellite rocket went wrong, with the booster and payload plunging into the sea.
State media blamed the setback on an unstable and unreliable new engine system and fuel.
It was not immediately clear if North Korea had used the Chollima-1 again, or a new system.
"I think it's plausible that they've resolved the likely cause of the stage separation issue they apparently encountered during the initial Chollima-1 launch attempt," Ankit Panda of the US-based Carnegie Endowment for International Peace told Reuters ahead of Thursday's launch.
"We've seen some static engine testing reported, which would be consistent with efforts to remediate problems related to the initial launch vehicle design."
Officials in Seoul, Tokyo and Washington DC condemned the May launch as a provocation and violation of United Nations Security Council resolutions banning the North's use of ballistic missile technology.
The secretive North considers its space and military rocket programs a sovereign right, and analysts say spy satellites are crucial to improving the effectiveness of its weapons.
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