"We're puzzled as to how they could be formed, how stable the configuration is, and why Jupiter's north pole doesn't look like the south pole," said Scott Bolton, Juno principal investigator from the Southwest Research Institute in San Antonio.
The results also showed that Jupiter's magnetic field is even stronger than models expected, and more irregular in shape.
Measurements of the massive planet's magnetosphere, from Juno's magnetometer investigation (MAG) indicates the magnetic field greatly exceeded expectations at 7.766 Gauss, about 10 times stronger than the strongest magnetic field found on Earth.
"Juno is giving us a view of the magnetic field close to Jupiter that we've never had before," said Jack Connerney, Juno deputy principal investigator and the lead for the mission's magnetic field investigation at NASA's Goddard Space Flight Centre in Greenbelt, Maryland.
Launched on August 5, 2011, Juno entering Jupiter's orbit on July 4, 2016.
The findings from the first data-collection pass, which flew within about 4,200 kilometres of Jupiter's swirling cloud tops on August 27, were published in the journal Science.
Juno is also designed to study the polar magnetosphere and the origin of Jupiter's powerful auroras -- its northern and southern lights.
These auroral emissions are caused by particles that pick up energy, slamming into atmospheric molecules.
Juno's initial observations indicate that the process seems to work differently at Jupiter than at Earth.
"We are excited to share these early discoveries, which help us better understand what makes Jupiter so fascinating," said Diane Brown, Juno programme executive at NASA Headquarters in Washington.
"It was a long trip to get to Jupiter, but these first results already demonstrate it was well worth the journey," Mr Brown said.
Juno is in a polar orbit around Jupiter, and the majority of each orbit is spent well away from the gas giant.
But, once every 53 days, its trajectory approaches Jupiter from above its north pole, where it begins a two-hour transit (from pole to pole) flying north to south with its eight science instruments collecting data and its JunoCam public outreach camera snapping pictures.
"On our next flyby on July 11, we will fly directly over one of the most iconic features in the entire solar system -- one that every school kid knows -- Jupiter's Great Red Spot. If anybody is going to get to the bottom of what is going on below those mammoth swirling crimson cloud tops, it's Juno and her cloud-piercing science instruments," Mr Bolton said.
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