The goal is to streamline four programmes totalling more than €143 billion in funding for innovation and research.
These include the Seventh Framework Programme for research (FP7), the Competitiveness and Innovation Framework Programme, the Cohesion Policy aimed at regions, and funds made available by the European Institute of Innovation and Technology.
The Commission invites comments via its innovation website until 20 May and will present new proposals in June. Key changes will be made after the current funding period, which ends in 2013.
"It will make sure each element of funding is contributing to tackling the grand challenges we face, in areas like climate change, energy and food security, resource efficiency, health or an ageing population," said Máire Geoghegan-Quinn, EU commissioner for research and innovation.
Currently, there is a risk of overlap between programmes, which have various and complex rules that have drawn criticism from participants.
The request for comment is spelled out in a green paper that follows last week's EU summit conclusions and the Commission's steps last month to simplify the Seventh Framework Programme, particularly for smaller companies, which are often at the forefront of innovation.
Streamlining 'long overdue'
"The idea is long overdue," said Ann Mettler, executive director of the Lisbon Council, a think-tank. "We need faster access to funds. A truly innovative venture is not going to sit around for two years and fill out forms."
The key, she said, is to have a performance measure and an impact assessment, and to ensure that the money is going to the most innovative companies.
"If it doesn't go to the best players, throwing money at innovation can distort the market."
The last time the Commission launched a similar call for comments, more than 1,700 organisations and individuals filled out an online questionnaire and more than 100 papers were submitted.
This time, the Commission will also hold a competition to choose a name for the new strategy, which is currently called the Common Strategic Framework. The Commission wants the new name to be more user-friendly and reflect the refocused funding for innovation and research.