The report outlines cases of athletes targeted for testing who "simply could not be found".
The report of the independent observers sent to the Games by WADA, by invitation of the International Olympic Committee, outlines cases of athletes targeted for testing who "simply could not be found".
A lack of adequately trained anti-doping personnel -- including chaperones to take athletes through test procedures -- contributed to the inability to meet daily targets for out-of-competition testing in the athletes' village.
"In fact, often only 50 percent or less of these planned tests were carried out," the report said.
Problems surfaced at competition venues as well, with chaperones denied access to some areas and therefore unable to accompany athletes throughout a test and many of the doping control officers were inadequately trained in sample collection and other procedures.
Despite the flaws, commission chair Jonathan Taylor said the anti-doping program in Rio "was able to achieve a number of positive outcomes in the face of very challenging circumstances".
"Despite staffing issues, resource constraints and other logistical difficulties, those tasked with implementation of the program, and in particular the volunteers, deserve immense credit for ensuring that the rights of clean athletes were safeguarded," Taylor said.
He also commended the IOC for its use of new techniques, including pre-Games testing and information gathering and the establishment of a new Court of Arbitration division to handle anti-doping cases as a first instance panel.
The report praised improvements made to Rio's anti-doping laboratory, which had been suspended by WADA just six weeks before the Games for failing to meet international standards.
The lab met requirements of WADA and the IOC -- including some prompted by the revelations of the McLaren Report about sample swapping at the Sochi Olympics laboratory -- and was "superbly equipped, operated very securely and generally very efficiently , and now represents an outstanding legacy from the Games for the anti-doping movement in South America," the report said.