The action came as ministers warned the summer's disaster will inevitably mean job losses across the region after meeting business leaders from the whole Yorkshire and Humber region.
Government business and enterprise secretary John Hutton, and minister for competitiveness Stephen Timms, heard of business' experiences of the floods before the protesters tried to get into the Directions Finningley building where the summit was held.
The protesters - members of the Campaign for Climate Action - arrived as the meeting was closing and police were called to clear them from the building.
It is the same organisation which has established a protest camp at Heathrow to fight the development of a proposed new runway.
The group's spokeswoman Christine Hooley said: "We're here because Yorkshire Forward are hosting the summit and it appears that, though the summit is about learning the lessons of the flood, they refuse to address the real issue - the link between the floods and climate change.
."It's ironic that the summit is being held at Finningley as the airport is part of the Government's plans to increase air use, as that is the fastest growing source of pollution in the UK.
Despite the disruption caused by the protesters, the event was hailed a success.
Doncaster's mayor Martin Winter said: "It was very useful for the various organisations to come together to see what lessons were learnt from the floods. The whole of Doncaster was significantly affected by the floods and we need to make sure that the individual businesses get the support they need."