The scheme has been branded a waste of time and money for failing to attract interest from the public.
On Tuesday, a special event was held in Brussels to mark the fifth anniversary of the initiative.
In the first five years of the ECI scheme the Commission said it had registered over 40 initiatives, which had collected over six million signatures.
But at the same time it also emerged that only three of these had actually gone as far as being formally considered by the Commission for discussion.
According to the executive, two of the three have seen concrete policy actions in response, including their inclusion in the Commission's 2017 work programme.
In a speech in Brussels at the annual European Citizens' Initiative Day, Commission First Vice-President Frans Timmermans announced that there were now plans to revise the scheme and "further improve the use of this important tool."
He said he wants to make the scheme more "citizen-friendly" and that there will also be a public consultation exercise before the summer recess.
Created by the Lisbon treaty and launched in April 2012, the European Citizens' Initiative was hailed at the time as an "agenda-setting tool in the hands of citizens."
The initiative aims to allow EU citizens to participate directly in the development of EU policies, by calling on the Commission to make a legislative proposal.
If a registered European Citizens' Initiative receives the signatures of one million validated statements of support from at least seven member states within a period of one year from the time it was registered, the Commission must decide whether or not it would act on it.
The Commission most recently registered two initiatives last month.
These concerned the rights of EU citizens in the context of the UK's withdrawal from the EU. It rejected a third proposal entitled 'Stop Brexit', saying that the conditions for registration had not been met.
In his speech, Timmermans said, "I want to make the ECI more accessible and citizen-friendly. I want the ECI to become a popular and living instrument, one that citizens are familiar with.
"There are obstacles to a more accessible and citizen-friendly ECI which have their origin in provisions of the ECI regulation itself. We should take a careful look at those too. This process could culminate in a proposal to revise the ECI Regulation this year."
The Commission, he said, will make proposals later this year, based on lessons learned in the five years since the regulation came into force, and drawing on a public consultation to be launched before the summer.
The event marking the fifth anniversary was organised by the EESC. Committee of the Regions President Markku Markkula and MEPs Soraya Post and György Schöpflin took part.
Debates at the ECI Day featured academics, representatives from EU institutions, civil society organisations, representatives of successful ECIs and other citizens' initiatives as well as citizens engaged in ongoing ECIs.
An EESC source said, "2017 is not only the 60th anniversary of the European Union; it is also the fifth anniversary of the European Citizens' Initiative Day - an opportunity to take stock and look at what has changed in term of citizens' participation."