Investigations by the European parliament and the Council of Europe have said that circumstantial evidence linked Warsaw and Bucharest to the programme.
Franco Frattini, the EU justice and home affairs commissioner, sent letters to the governments of Poland and Romania in July, pressing for in-depth judicial inquiries.
Frattini asked for clarification on "allegations of detention centres in these countries".
Johannes Laitenberger, the EU commission spokesman, said: "We have not received a reply from Poland, and the information from Romania was not considered complete. Frattini sent reminders in January and we're currently awaiting replies."
No deadline for a response has been set.
Both Romania and Poland have resolutely refuted accusations of hosting secret CIA prisons and supporting rendition flights.
EU human rights laws state that any involvement in rendition flights is illegal.
The European parliament and the Council of Europe have singled out 14 European nations for playing a role in the CIA programme, which was initiated after the September 11 attacks on the US.