Media regulator Ofcom has so far received 10 complaints about an item in last night's programme, while 81 viewers have complained directly to the BBC -- these figures are expected to rise throughout the course of the day.
The incident comes just two weeks after the programme was slammed for making light of car accidents, with coverage of Richard Hammond's crash condemned by road safety charities as "very irresponsible".
Last night's episode, an American fly-drive special, saw presenters Clarkson, Hammond and James May buy a $1,000 car in Miami and drive it 800 miles to New Orleans.
Clarkson picked a Chevy Camaro, while Hammond was in a pick-up truck and James May in a Cadillac. All three took a pit stop in Mississippi, where producers challenged them to make dinner from roadkill.
After a dead squirrel failed to whet their appetites, Clarkson returned with a deceased cow strapped to his roof. While Hammond and May descended into hysterics, Clarkson rapidly reversed and turned the car, to make the dead animal fall off.
Jan Creamer, chief executive of Animal Defenders International, said: "In this case, it is not a matter of whether the animals suffered for the programme, but the fact that 'Top Gear' is making light of an activity that is so demeaning to animals.
"Top Gear is being completely irresponsible promoting this activity. Our message is simple. If a family programme like this thinks it is reasonable to degrade animals in this way to endorse such unthinking attitudes to our fellow creatures, then we must encourage viewers to boycott it."
However, the BBC is standing by the programme, and a spokesman said: "We've had just over 80 complaints about the dead cow on the roof for an audience averaging 6m viewers.
"Viewers are well aware of the type of humour on 'Top Gear 'and this was very typical of its irreverent humour. However, no offence was intended."
Ofcom may now investigate the programme in reference to section 2 of its broadcasting code. Section 2 is in place to provide "adequate protection for members of the public from the inclusion of harmful and/or offensive material."
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