The vote on January 23 was 125 votes to 79.
The report was prepared by German Social Democrat Christoph Strasser, who has drawn up a list of 85 alleged political prisoners in Azerbaijan.
On January 23, in an addendum to the report, Strasser said 35 of the people on the list had since been released.
Azerbaijan's delegation has strongly opposed the report.
Delegates from a number of other countries had also voiced doubts about its usefulness, citing persistent ambiguities about the definition of a political prisoner as well as questions about whether some on the list are in prison.
Strasser, who was denied entry into Azerbaijan, has demanded that Baku resolve the cases of the people on the list without demanding admissions of guilt or public repentance as a condition.