The spots appear on the side of Pluto that always faces its largest moon, Charon - the face that will be invisible to New Horizons when the spacecraft makes its close flyby on July 14, NASA said.
New Horizons principal investigator Alan Stern of the Southwest Research Institute, Boulder, Colorado, described the image as "the last, best look that anyone will have of Pluto's far side for decades to come."
"It's weird that they're spaced so regularly," said New Horizons programme scientist Curt Niebur at NASA Headquarters in Washington.
"We can't tell whether they're plateaus or plains, or whether they're brightness variations on a completely smooth surface," said Jeff Moore of NASA's Ames Research Centre, California.
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The large dark areas are now estimated to be 480 kilometres across, an area roughly the size of the state of Missouri.
In comparison with earlier images, we now see that the dark areas are more complex than they initially appeared, while the boundaries between the dark and bright terrains are irregular and sharply defined, NASA said.
"When we combine images like this of the far side with composition and colour data the spacecraft has already acquired but not yet sent to Earth, we expect to be able to read the history of this face of Pluto," said Moore.
When New Horizons makes its closest approach to Pluto, it will focus on the opposing or "encounter hemisphere" of the dwarf planet.