Earlier this year, the Council of Europe accused both Romania and Poland of allowing the CIA to run detention centres between 2003 and 2005.
The European Justice Commissioner, Franco Frattini, asked for an explanation from both countries.
He is still awaiting a response from Poland.
Global spider's web
The report from the Council of Europe, led by the Swiss senator Dick Marty, said the prisons were part of a "global spider's web" involving detentions and illegal flight transfers known as extraordinary renditions.
A Romanian spokeswoman in Brussels, Doris Mircea, said that a committee of inquiry set up by the government had concluded that the allegations were unfounded.
She said that the letter to the European Commission emphasised that "no person was kept illegally as a prisoner within Romanian jails and no illegal transfer of detainees passed through Romanian territory".
In June, the former Polish president, Aleksander Kwasniewski, denied there had been any kind of secret CIA prisons in Poland or that there had been any discussion of the matter.