Responding to questions by Spanish green MEP Raul Romeva i Rueda and Portuguese far-left deputy Rui Tavares at her parliament hearing in Brussels on Tuesday (12 January), Ms Reding voiced concern over the idea of putting body scanners at airports and EU plans to share people's private data with US intelligence agencies.
"We will not let anyone dictate to us rules that go against fundamental rights on anti-terrorism grounds ...our need for security cannot justify any violation of privacy. We should never be driven by fear, but by values," she said.
"During the last decade the concentration has been on security alone, justice was neglected."
US authorities have in the wake of a failed Christmas Day bomb plot begun buying hundreds of x-ray body scanners which show passengers' 'naked' bodies, putting pressure on the EU to follow suit.
The initiative comes on top of previous US calls for EU access to citizens' financial data via the "Swift" banking system and private travel details, or "PNR" records.
The UK, the Netherlands and Italy backed the use of scanners at an EU aviation security meeting last week. But Belgium, Spain and Germany voiced scepticism, with the EU commission tasked with exploring a potential bill on making body scans mandatory across the union.
Ms Reding said scans should remain voluntary for now with further studies needed to prove their usefulness.
"We have to look at less intrusive and more privacy friendly ways to detect explosives," she explained. "Do those scanners work efficiently, do they pose health risks, do they have specific problems for privacy, for data protection?" she asked.
Ms Reding promised to push the EU's Charter of Fundamental Rights as a new criterion in the commission's future impact assessment studies of all new legislation and to publish an annual report on countries' compliance with the code.
In terms of other judicial priorities, Ms Reding said she would look into establishing an EU-level public prosecutor to focus on cross-border financial crimes, design new EU-wide copyright-protection measures and push to close the gender pay cap.
The outgoing telecoms commissioner pointed to her attack on mobile phone companies' roaming fees as proof of her tough approach to corporate vested interest.
The German Pirate Party organised naked protests against scanners at airports in the country last weekend