The drill bit on the Curiosity could possibly be contaminated with Earth microbes after the last drill was added in an unsterile environment - sparking fears we may end up 'contaminating Mars with life' if the drill touches water, the Los Angeles Times reported.
Scientists have chosen the cold, dry equatorial landing site in Mars' Gale Crater to study the geology of the Red planet, not to find its prospects for harbouring water or ice.
However, if the rover does find water, a controversy that has simmered at NASA for nearly a year will burst into the open, the report said.
Curiosity's drill bits may be contaminated with Earth microbes and if those bits touch water, the organisms could survive.
The possible contamination of the drill bits occurred six months before the rover's launch last November 26. The bits had been sterilised inside a box to be opened only after Curiosity landed on Mars.
The engineers grew concerned that a rough landing could damage the rover and the drill mechanism so they decided to open the box and mount one bit in the drill as a hedge to ensure success of one of the most promising scientific tools aboard Curiosity.
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The drill is to bore into rocks looking for clues that life could have existed on the planet. Even if a damaged mechanism couldn't load a drill bit, at least the rover would have one ready to go.
Under the agency's procedures, the box should not have been opened without knowledge of a NASA scientist who is responsible for guarding Mars against contamination from Earth. However, Planetary Protection Officer Catharine Conley wasn't consulted.
"They shouldn't have done it without telling me. It is not responsible for us not to follow our own rules," she was quoted as saying by the paper.
The rules required sterilisation of any part of Curiosity that will touch the surface of the planet, including the drill bits and all six of the rover's wheels.
The precaution was taken to preserve the ability to explore water or ice - even if the chances of finding it were remote.
Conley, a microbiologist, said she learned about the unsealing of the box shortly before the launch. By then, it was too late to fix.
Other NASA officials said the decision to open the box of drill bits was a calculated risk.
"Water or ice near the surface in Gale Crater was not a significant probability," David Lavery, program executive for solar system exploration at NASA headquarters, said.
"We weighed that against the risks of not having a bit mounted in the drill prior to launch, and the specter of not being able to drill any holes at all on Mars," Lavery added.