In September, George Bush, the US president, acknowledged that terrorism suspects have been held in CIA-run prisons overseas, but did not say where.
Last month, Britain's government said it had known "in general terms" about a secret CIA prison network.
The EU draft report gives no direct proof that the CIA ran secret prisons in Europe - an allegation that prompted the inquiry in November 2005 - but accuses 11 EU governments and some officials, including Javier Solana, the EU foreign policy chief, of not co-operating with the investigation.
On Wednesday, the European parliament will hold a final vote on the report, but before that they must contend with 270 tabled amendments, many proposing to soften the report's criticism.
Legislators said the most controversial sections of the report would probably have to be toned down before it could gain cross-party support in the 785-seat EU assembly.
No EU governments have admitted that the alleged anti-terror operations were being carried out on their soil.
Human Rights Watch identified Poland and Romania as possible locations of secret prisons, but both countries denied involvement and the report says the claims could not be proven.
The conservative European People's Party, the EU legislature's largest political grouping, called the EU draft report biased and said it wanted major changes.
"The report lacks objectivity. In its present form it's useless," Jas Gawronski, Italian conservative deputy, said, adding that it contained little hard evidence that EU members knew about the alleged secret CIA flights.
He said he wanted the report to recognise that the CIA has the right to "fly wherever and whenever necessary, to land at European airports using its own aircraft or those of private companies, and to transport any kind of passengers in the absence of any infringement of law".
Such a statement would appear conciliatory, after committee members made headlines over the past year accusing EU member states of helping the US transport terror suspects to secret prisons overseas in breach of European civil liberties standards.
Even the Socialists, who had backed using strong language in condemning EU countries, have proposed softening the criticism against EU leaders and governments - primarily to ensure it passes through the parliament.
The changes would include removing criticism of Britain for alleged non-co-operation with the committee, and softening criticism of Germany for spurning an early US offer to free a Guantanamo Bay prisoner - to ensure British and German support for the report.
Another amendment erases all criticism of Solana, who had called the report's claim that he had made omissions and denials in his testimony "completely wrong and unfair".