"We have a very serious anomaly on the vehicle," Pete Theisinger, project manager for the Mars Exploration Rover mission said.
Officials of the National Aeronautics and Space Administration had earlier said thunder and lightning storms over Australia had prevented scientists from sending Spirit its daily instructions.
But now they think the problem could be much more serious.
Theisinger said NASA experts have sent a command to Spirit but are not sure if they got an acknowledgement.
"I am told that they think they got it, that would mean that the spacecraft thinks it is on the fault side of the tree for some reason, that would mean we have got positive power, some elements of the software are working. So that would be good news, but again, we need to confirm that."
"We have a very serious anomaly on the vehicle"
Project manager, NASA
Theisinger said NASA was "very concerned."
Spirit arrived on Mars on 3 January and started searching for signs of past life on the red planet last week.
Its twin rover, Opportunity, is due to touch down this weekend. The $820 million mission expects each solar powered robot to keep working for about three months.
NASA stopped communicating with Spirit at about 1440 GMT on Wednesday.
Engineers first noticed the problem when they tried to send instructions to Spirit.
NASA usually sends daily instructions to the rover and Spirit sends back information several times a day using two US satellites orbiting Mars.