Georgia Georgladou told a hearing in Parliament on Thursday the Commission was currently "assessing the scope" of any possible legislation.
"We are looking at where gaps exist but we have to respect the subsidiarity principle," said the official, who is a deputy unit head and deals with fundamental rights policy.
"There will be an in-depth legal analysis but the commission strongly supports greater protection for people who seek to expose wrong doing, including tax evasion."
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The hearing was hosted by the Socialist group and also heard calls from several other speakers, including Janina Berg, an anti-corruption campaigner, who urged the commission to produce a directive giving whistleblowers more legal protection.
She said whistleblowing should be encouraged as it is a "form of free speech."
"A directive would be one of the best possible tools in tackling wrong doing, which is not just about tax but a whole range of other criminal activities."
Berg highlighted the recent 'Swiss leaks' case as an example of how whistleblowing can "shed the light" on wrong doing, including arms trafficking and bribery.
Martin Jefflen, President of Eurocadres trade union, echoed her demand and pointed to a new platform recently launched to encourage people to report wrongdoing within the EU and elsewhere.
He said, "Greater legal protection for whistle blowing would give people more confidence about coming forwards."
The meeting on Thursday comes in the wake of the LuxLeaks scandal which resulted in MEPs setting up two special committees on tax rulings.
EULEAKS (euleaks.eu), recently launched, is an online platform which will allow whistleblowers to upload documents securely and anonymously.
Sven Giegold, one of several MEPs behind the initiative, said, "The aim is to better protect whistleblowers."Giegold said, "This web portal will allow whistleblowers to submit messages and documents anonymously to us at the highest possible security standards.
"With 'EU Leaks' we provide a platform for people who are no longer willing to accept scandals against the common good.”
Other Greens/EFA group members involved include Pascal Durand, Bas Eickhout, Benedek Jávor, Eva Joly, Ernest Maragall, Michel Reimon, Molly Scott Cato, Bart Staes, and Ernest Urtasun.
They also include Philippe Lamberts, Co-President of the Greens/EFA Group, who said, "With the help of whistleblowers we would like to uncover breaches of the law, misconduct, abuse of power, incompetence, discrimination and so forth in relation to EU law, in the EU institutions, enterprises and the member states.
"Any information we receive will be analysed and in all probability used politically for making Europe better. We want to ensure that European values and laws are treated with utmost respect."
A Greens/EFA spokesperson said, "We have already presented a proposal for a draft EU directive ensuring an effective protection of whistleblowers at EU level. We will continue calling for a secure legal framework.
"More and more supporters from all political groups in the European Parliament are joining this initiative. It is high time that the commission put forward a proposal for the European protection of whistleblowers."