The massive storm system is about 9,000 kilometres in length, or one-third the size of Neptune's radius, spanning at least 30 degrees in both latitude and longitude.
Ned Molter from University of California, Berkeley in the US observed the storm getting much brighter between June 26 and July 2.
"Seeing a storm this bright at such a low latitude is extremely surprising," said Molter, who spotted the storm near Neptune's equator during a dawn test run of twilight observing at W M Keck Observatory on Maunakea, Hawaii.
"Historically, very bright clouds have occasionally been seen on Neptune, but usually at latitudes closer to the poles, around 15 to 60 degrees north or south," said Imke de Pater, a professor at UC Berkeley.
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"Never before has a cloud been seen at or so close to the equator, nor has one ever been this bright," said de Pater.
At first, de Pater thought it was the same Northern Cloud Complex seen by the Hubble Space Telescope in 1994, after the iconic Great Dark Spot, imaged by Voyager 2 in 1989, had disappeared.
A huge, high-pressure, dark vortex system anchored deep in Neptune's atmosphere may be what is causing the colossal cloud cover, said de Pater.
As gases rise up in a vortex, they cool down. When its temperature drops below the condensation temperature of a condensable gas, that gas condenses out and forms clouds, just like water on Earth. On Neptune, however, methane clouds form.
As with every planet, winds in Neptune's atmosphere vary drastically with latitude, so if there is a big bright cloud system that spans many latitudes, something must hold it together, such as a dark vortex. Otherwise, the clouds would shear apart, researchers said.
If it is not tied to a vortex, the system may be a huge convective cloud, similar to those seen occasionally on other planets, like the huge storm on Saturn that was detected in 2010.
However, such a cloud would be expected to smear out considerably over a week's time, researchers said.
"This shows that there are extremely drastic changes in the dynamics of Neptune's atmosphere, and perhaps this is a seasonal weather event that may happen every few decades or so," said de Pater.