Politicians have "a duty to listen" to the public's opinion, Cabinet minister Ruth Kelly said, as a petition on the Downing St website continues to grow.
Downing St set up online petitions in November 2006
The petition calling for the planned road pricing scheme to be scrapped has gathered more than 1.27m signatures.
According to the Daily Mail, a senior minister said whoever came up with the idea to let people create petitions on Number 10's website was "a prat".
But Ms Kelly said it was part of a "long history of popular movements".
Transport Secretary Douglas Alexander said the road-pricing petition, which closes on 20 February, would be part of the debate on the issue.
Asked on BBC Radio 4's Today programme if such petitions would inform policy making, Ms Kelly said: "I think it's a good test of public opinion on a particular issue, but what they don't judge is the overall terms of the debate, the choices that politicians have to make in a representative democracy."
The Daily Mail reported on Tuesday that as the Downing Street website crashed after so many people wanted to add their names to the petition, one minister said: "Whoever came up with this idea must be a prat".
But Ms Kelly said: "I don't recognise that description.
"I certainly wouldn't have said that, but the fact is we need to be able to be out there talking to people, to judge their opinions, to take them with us as we engage in really difficult decisions."
Downing St set up its "e-petition" section in November 2006, where the public can create petitions and sign existing ones.
Petitions and protests
There are currently 2,925 open petitions, 304 closed petitions and 610 rejected petitions.
Ms Kelly said "There's been a long history of popular movements in democracy in this country. People in the past may have engaged in protests.
"Petitions are another way of doing that and we as politicians have a duty to listen to the points that are being made, to take them into account and to think about how we frame our argument .
"But the fact is, whether it's on road pricing or on social homes and housing, the status quo is not an option. We have to respond to the other legitimate expectations that are out there too."
The campaign group Unlock Democracy said the Downing Street petitions which gained more than 100,000 signatures should be independently examined by a "citizen jury".
"In the longer term, rather than being put off from this experience, the government should embrace the hunger for more direct democracy and introduce a system of citizen-led initiatives and referendums," said director Peter Facey.