On Thursday afternoon, they said they hadn't had any contact with the vehicle for 24 hours and that they couldn't yet explain what was causing the problem.
Spirit was expected to search for signs of life for the next three months. Its twin robot - called Opportunity - is set to land on Mars at the weekend.
UK scientists failed to contact their robot - Beagle 2 - earlier this month.
But everything had been going well for Spirit.
It managed to move off its landing pod and had sent back some spectacular images of the red planet.
At first, scientists thought the breakdown in communication was because of thunder storms over Australia.
But it now seems that the problem could be more serious.