The papers - some marked Top Secret - include transcripts in German and English and additional material, which researchers believe could cast new light on the trials of the Nazi hierarchy.
The first instalment, entitled "The Nazi Master Plan; The Persecution of Christian Churches", shows how the Nazis planned to supplant Christianity with a religion based on racial superiority.
The report, prepared by the Office of Strategic Services - a forerunner of the CIA - says: "Important leaders of the National Socialist party would have liked... complete extirpation of Christianity and the substitution of a purely racial religion."
"The best evidence now available as to the existence of an anti-Church plan is to be found in the systematic nature of the persecution itself," it said.
"Different steps in that persecution, such as the campaign for the suppression of denominational and youth organisations, the campaign against denominational schools, the defamation campaign against the clergy, started on the same day in the whole area of the Reich...and were supported by the entire regimented press, by Nazi Party meetings, by travelling party speakers."
The documents - with original handwritten notes - appear on the web site of the Rutgers University School of Law in New Jersey in the United States.
The 148 volumes of material, which will be published in parts every six months, were compiled by General William J Donovan, an investigator at the International Military Tribunal in Nuremberg after World War II.
General Donovan supplemented the trial documents with his own notes, drawings, photographs and letters, which researchers say provide new insights into the trials.
New perspective
Project editor Julie Seltzer Mandel believes the first instalment presents a different perspective on Nazi persecution.
"A lot of people will say, 'I didn't realize that they were trying to convert Christians to a Nazi philosophy', Ms Mandel, a third year law student, told Philadelphia's The Inquirer newspaper.
"They wanted to eliminate Jews altogether, but they were also looking to eliminate Christianity."
The next set of papers, to be posted in six months, will be drawn from a secret OSS document entitled "Miscellaneous Memoranda on War Criminals". It documents the efforts made by various nations to capture and prosecute Nazis.
A third instalment, to go online in a year, reveals confidential Nazi orders. Included are instructions for the infamous Kristallnacht ("Broken Glass Night").
A message entitled "Measures To Be Taken Against Jews Tonight" informed Nazi authorities that "Jewish shops and homes may be destroyed, but not looted....Foreigners, even if Jewish, will not be molested".