The European commission has raised concerns directly with the US administration about the threat posed to the privacy of EU citizens from the sort of data monitoring highlighted by the leaking of NSA documents to the Guardian by the whistleblower Edward Snowden.

Viviane Reding, the vice-president of the commission who is in charge of justice, challenged the US attorney general, Eric Holder, at a meeting in Washington last month and will raise the matter again at an EU-US meeting on Thursday in Dublin.

Mina Andreeva, the commissioner's spokeswoman, told The World at One on BBC Radio 4: "The European commission is concerned about the possible consequences on EU citizens' privacy.

"The commission has raised this systematically in its dialogue with the US authorities, especially in the context of the negotiations of the EU-US data protection agreement in the field of police and judicial co-operation, where the draft text has been on the table now for two years.

"This was also raised, by the way, by Vice-President Reding at her last meeting with US attorney general Holder in Washington in April. The vice-president will again raise this with her American counterparts at the upcoming EU-US ministerial meeting on 13-14 June in Dublin."

The intervention by the commission follows a warning by a senior member of the European parliament that the EU would redouble its efforts to strengthen the proposed EU-US agreement, in the light of the Guardian disclosures. Hannes Swoboda, leader of the socialist group in the parliament, told the FT: "With all the information we've found out in recent days about how easily the US spies on people's private data I think it will be difficult for the Americans to oppose a strong data protection agreement.

"This issue is very critical for us in Europe … There will be growing resistance against an agreement with the US unless there are some clear guarantees from their side that our European principles of data protection are respected."

Reding's spokeswoman was critical of some EU member states, believed to include Britain, which she said showed little appetite for protecting privacy, and were pressing ahead with introducing new powers to give states greater access to data.

Andreeva said: "National security is a matter for the member states, but this case goes to show that a clear legal framework for the protection of personal data is not a luxury or not a constraint: it is a fundamental right. This is exactly the spirit of the EU's data protection reform that has been on the table for 18 months and where we see that some member states are not moving very enthusiastically towards adopting this reform swiftly.

"But in turn they give a lot of priority to legislation – notably the data retention directive that was negotiated in a record time of six months, which allows you to limit civil liberty rights of consumers. So I think it is high time that we move up a gear, that member states move up a gear and show their commitment in protecting EU citizens' fundamental rights and privacy rights in the 21st century."