Leila Deen from campaign group Plane Stupid said she was protesting at reports that Lord Mandelson met lobbyists from Heathrow owner BAA before the Government gave the controversial go-ahead for a third runway at the London airport.
The incident happened a few seconds after Lord Mandelson got out of his ministerial car to attend the summit in central London.
Ms Deen, 29, threw a cup full of what she described as "green slime" over the minister, who tried to duck when he realised what was happening.
Ms Deen, who calmly walked away after the incident, said: "The only thing green about Peter Mandelson is the slime coursing through his veins."
Lord Mandelson dismissed the incident, which raises questions about his personal security, as an "adolescent protest".
He told Sky News: "She was so busy throwing what seemed like green soup or something in my face that she failed to tell me what the protest was about but, as you can see, thankfully it wasn't paint and I've come through it intact."
Ms Deen questioned the Business Secretary's attendance at the summit.
"That Mandelson is trying to make political capital out of climate change just days after reports that he met with BAA's top lobbyists to push through the third runway is an insult to my generation," she said.
Ms Deen accused Lord Mandelson of only representing business interests, adding that he was an unelected Government representative.
Lord Mandelson quickly walked into the building where the summit is being held after the incident and emerged a few minutes later, minus his coat.
Prime Minister Gordon Brown was also due to attend the summit along with other Government representatives and business leaders to discuss the "greening" of industry and opportunities for new jobs.
Plane Stupid has launched a series of high profile stunts in recent years against the Government's environmental policies.
Ms Deen was one of three Plane Stupid protesters who sounded horns during a speech at an environmental conference in London by Transport Secretary Geoff Hoon earlier this week.
She and the other demonstrators left after being warned they would be thrown out if they interrupted the speech again.
At one point they sounded horns when Mr Hoon reached the part of his speech when he said that proper debate rather than "stupid stunts" was the way to address the aviation-and-the-environment issue.
Ms Deen added later: "We know that Mandelson is best buddies with BAA's top lobbyist Roland Rudd, and reports suggest it was him who bullied
Energy Secretary] Ed Miliband into accepting a third runway. We can't let the Prince of Darkness cast his shadow over west London."
A Scotland Yard spokesman said no arrests had been made and an investigation would only be launched if a complaint was received.
Ms Deen told the Press Association later that the substance she threw at the minister was custard, which had green colouring added to it.
"Peter Mandelson is trying to say he doesn't know what it was about, but as I threw it I said 'This is for the third runway'.
"He knows he is in bed with business, working against the interests of the climate and the people of this country.
"He was trying to make political capital out of this summit but we are just not prepared to let him get away with it."
Ms Deen, originally from Brighton, has been an activist for several different campaigns since her days at Leeds University, where she read development studies and politics.
Gordon Taylor, who lives next door to her family home in Valley Drive, Brighton, said: "I think her mother would be proud.
"Nothing surprises me these days. We rarely see Leila since she left home to attend university in her teens but I am aware that she has fought for a number of causes over the years."
Lord Mandelson said at the summit: "Low carbon is not a sector of our economy, it is, or will be, our whole economy, and a global market.
"Today we are asking what more needs to be done to ensure these changes benefit the UK economy, and what needs to be done to equip British companies to compete for low carbon business in Britain and overseas.
"A low carbon industrial strategy must seize the opportunities that will come with change. That requires a new industrial activism for a new green industrial revolution."
Mr Miliband said: "Tackling climate change doesn't just make moral sense, it makes economic sense too.
"The shift to low carbon in the UK, and around the world, is now largely inevitable. What is not inevitable is that Britain benefits industrially from the transition. We want to mobilise every bit of expertise and ingenuity that Britain has to offer.
"Moving to a low carbon economy is the way to secure the economic recovery and growth we need at home and take a lead internationally to protect the future of the planet."
Independent research presented to the summit showed that the UK was the 6th largest low carbon and environmental goods and services economy.
In 2007/8 it was worth 107 billion to the UK economy, and could grow by another 45 billion over the next decade.
There are more than 880,000 jobs in the low carbon environmental goods and services sector when the supply chain is included. If employment grows at projected rates, an additional 400,000 jobs could be created in the next decade, said the report.