It was claimed that the system used to ignite MPL's hydrazine fuel could not have coped in the extreme cold of space and that the engines were only installed in the spacecraft after an unnamed individual had falsified test data.
It was said that Nasa officials hid the facts from the public when they discovered what had happened in the tests.
Contact was lost with MPL on 3 December when it turned to enter the Martian atmosphere. Two microprobes were also lost in the descent.
But the space agency utterly rejected the claims, which had been circulating as rumours before appearing in wire reports on Tuesday.
Nasa spokesman Don Savage said they were not clear about what caused the Mars Polar Lander to disappear as it approached the Martian surface and rejected the earlier claims of a cover-up.
However, BBC News Online science editor David Whitehouse said a report due next week on the loss of the spacecraft would be one of the most damning in Nasa's history, and was likely to catalogue many failures.
Nasa said the concerns relating to the cold firing of the thrusters had been publicly aired in November, almost a month before MPL reached the Red Planet.
'Complete nonsense'
These concerns were raised by Art Stephenson who led the panel called in to investigate the loss of the sister mission Mars Climate Orbiter back in September.
As a result, MPL engineers took the decision to switch on heaters several hours prior to the spacecraft's entry into the Martian atmosphere. This would have raised temperatures to eight degrees Celsius - well above -20 degrees Celsius which was shown subsequently to be the lowest acceptable operating temperature.
Nasa said both Stephenson's team and another review team headed by the Jet Propulsion Laboratory's John Casani had "surfaced no evidence relating to thruster acceptance testing irregularities".
The agency said "members of the review teams are using words like 'bunk', 'complete nonsense', and 'wacko', to describe their reactions" to the idea.