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The attack came as Lord Mandelson arrived at the launch of the Government's low carbon economy summit in London on Friday morning.
Leila Deen, an activist from the campaign group Plane Stupid, was behind the stunt, according to the group. The protest was part of an ongoing campaign against the proposed third runway at Heathrow airport.
After the incident, Lord Mandelson said: "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 is wasn't paint and I've come through it intact".
Miss Deen, originally from Brighton, said 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."
She told BBC News: "It is a lighthearted way of making a very serious point. All of our MPs have let us down.
"I don’t want to wake up early to throw green custard over Peter Mandelson. But something has to protect our children’s future.
"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."
Later, she commented: "I am sure Mandelson would have preferred it if it was guacamole."
Miss Deen 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."
A Scotland Yard spokesman said no arrests had been made and an investigation would only be launched if a complaint was received.
Miss 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.
Earlier this week Scottish police arrested nine environmental activists who broke through a fence at Aberdeen airport to protest expansion plans, dozens of flights were cancelled.
The demonstrators were dressed as golfers, a reference to real estate magnate Donald Trump's plans to build a controversial golf resort in the area.
The group Plane Stupid also disrupted operations in December at Stansted airport in a protest against a possible second runway and escalating carbon emissions. Again, many flights were cancelled and police made arrests.
Prime Minister Gordon Brown later made light of the protest.
Addressing the carbon summit he said: "If anybody doubted the greening of Peter Mandelson and his willingness to take the green agenda on his shoulders we've seen it in practice on our television screens already this morning."
Mr Brown told the summit that moving Britain to a low carbon economy will create 400,000 new "green" jobs over the next eight years.
Mr Brown is calling for an international "green new deal" to boost the environmental sector and help lift the global economy out of recession.
He was due to release independent research which, the Government says, shows a total of 1.3 million people will be employed in the environmental sector by 2017 - representing an annual growth rate of 5%.
Before arriving at the event, Lord Mandelson said the announcement was "not simply a green job creation exercise or a way of greening the economic recovery from our current recession".
Cutting carbon by implementing cost effective energy saving measures is expected to save business billions in reduced energy use, the Government has claimed.
Lord Mandelson told BBC Breakfast it was a "really important low carbon technological and industrial revolution that is going to sweep across the global economy during this century."
