Asian space race
Friday's launch is the latest in a new race to the Moon, with China, India and the US also planning lunar missions.
Japan has been expanding its space operations and aims to send an astronaut to the Moon by 2025.
Tatsuaki Okada, a scientist involved in the $479m project, said: "If we succeed in this programme, we will be able to prove that Japan has the technology."
The Selene mission is four years behind schedule due to rocket failures and technical glitches, the Japanese space agency said.
In November 2003, Japan was forced to destroy a rocket carrying a spy satellite 10 minutes after lift-off when a rocket booster failed to separate.
The setback came just a month after neighbouring China became the third country to carry out a manned space mission.
China is pushing ahead with plans for a lunar mission later this year, and aims to land an unmanned vehicle on the Moon by 2010.
India is planning its first unmanned mission to orbit the Moon in 2008, powered by a locally built rocket, and is also considering sending a person to the Moon by 2020.
The US plans to launch a lunar orbiter next year.
'Princess' lifts off
Japan's orbiter, named Kaguya, will gather data on chemical element distribution, mineral distribution, topographical and surface structures, the gravity field and the environment of the Moon.
Kaguya is named after a beautiful princess who according to Japanese folklore charmed many men before ascending to her home, the Moon.
Eriko Sunada, an agency spokeswoman said the launch had proceeded smoothly.
"We successfully launched the rocket and released the orbiter from the rocket," she said in Tokyo.
The explorer consists of a main unit and two small satellites equipped with observation instruments designed to examine the Moon's surface terrain, gravity and other features.
It will travel around the Earth twice before the main unit moves into orbit 100km above the Moon in early October.