The fire, which was followed by an explosion and plumes of white smoke, followed an explosion last year by the same Epsilon S engine during a test, Japan's Kyodo news agency reported.
JAXA has investigated the extent of illegal access while shutting down the affected networks and verifying that they did not contain classified information about the operations of rockets and satellites and national security.
The H3 had a "successful liftoff" at 9:22 a.m. Tokyo time (0022 GMT) and was "on course" with its engines properly working, JAXA said in a live broadcast that showed scientists clapping and hugging each other at Tanegashima Space Center.
Japan's "Moon Sniper," the Smart Lander for Investigating Moon (SLIM), successfully landed on the lunar surface, achieving a pinpoint soft landing about 55 meters from its target.
According to NASA, the satellite and its two instruments will observe the universe’s hottest regions, largest structures and objects with the strongest gravity.
After swooping past Mercury at altitudes of under 200 kilometers (125 miles), the spacecraft took a low resolution black-and-white photo with one of its monitoring cameras before zipping off again.
Japan made it to history books last week when it became the first country to successfully land on the surface of asteroid Ryugu
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