A Clarence House spokesperson confirmed the attack and said the heir to the throne and his wife were unharmed.
A photographer with The Associated Press reported seeing demonstrators kick the prince's car. Photos in Britain's Daily Mail show that the car was hit with paintballs.
The royal couple was on their way to a performance of the Royal Variety show, the spokesperson told ABC News.
Click here for images of the London protests.
One witness to the attack on the prince and his wife told the BBC that he saw "a couple of people were kicking the door."
I didn't see who done the graffiti, I didn't see who smashed the window," the witness said, "but I saw Prince Charles in his car get attacked. It was Prince Charles in the car, it was - I couldn't believe it."
The incident was an example of how heated the protests over tuition hikes have gotten. Protestors today smashed windows, threw flares and tussled with police. The Daily Mail called the protestors "anarchists."
The British newspaper reported that tens of thousands of people were protesting the government's decision to raise the cap on student tuition from 3,290 pounds 9,000 pounds, or about $14,160.
Though one protestor told the Daily Mail the demonstration was originally "like a carnival," the mood turned ugly and the streets became dangerous for police and protestors.
Police told The Associated Press earlier today that there had been seven arrests; 13 protesters and eight officers had been injured.
Photos Show Dangerous Clashes in London
Pictures of London today showed police officers being yanked off their horses by protestors and emergency workers tending to both injured officers and civilians.
One woman was even photographed swinging from a Union flag.
Much of the protestors' anger was directed at Deputy Prime Minister Nick Clegg, who signed a pre-election promise to avoid such hikes.
"I'm here because the Liberal Democrats broke their promise," said 19-year-old college student Shivan David from London's Trafalgar Square. "I don't think education should be free but I do think that tripling fees doesn't make any sense. We are paying more for less."
London authorities grappled with a similar, though much smaller protest last month.
Theater student Bebe William Daniels told ABC News in November that she was willing to risk arrest to stand up to politicians.
"They don't listen to us, we don't have a vote on this and this is the only way we can show people how much we care," Daniels said.