Enigmatic traces of water in the upper atmosphere of Jupiter came from a comet that crashed into the giant planet in 1994, the European Space Agency (ESA) said on Tuesday.

Astronomers have been debating the water for 15 years after telltale molecules were spotted by an infrared telescope.

Some argued the water brewed up from lower levels of the gassy planet, but others said it could not have crossed a "cold barrier" separating the stratosphere from the cloud level below.

ESA's deep-space Herschel telescope has now found that most of the water is concentrated in Jupiter's southern hemisphere.

The molecules are clustered at high altitude around the sites where 21 fragments from Comet Shoemaker-Levy 9 whacked into Jupiter in July 1994 in one of the most spectacular recorded events in astronomy.

The collisions left dark scars in Jupiter's roiling atmosphere that persisted for weeks.

"According to our models, as much as 95 percent of the water in the stratosphere is due to the comet impact," said Thibault Cavalie of the Bordeaux Astrophysics Laboratory in southwestern France.

Other potential sources, including water vapour disgorged by one of Jupiter's icy moons or interplanetary particles of icy dust, can be ruled out, he said in a press release issued by ESA.

The study appears in the European journal Astronomy and Astrophysics.

Comets are believed to be primeval balls of ice and dust left over from the building of the Solar System.

Cometary bombardment is believed by some experts to have provided the infant Earth with its abundance of water, the stuff of life.