WASHINGTON — A trove of documents housed in a secure vault at the John F. Kennedy Library has long been described as Robert F. Kennedy’s private papers and been kept from public view by the Kennedy family. But many of the documents have little to do with personal matters and instead detail once-secret military and intelligence activities he helped manage as attorney general, according to an unpublished index of the collection obtained by The Boston Globe.

Scholars and government officials believe the 62 boxes of files covering Kennedy’s three years as attorney general during his brother’s administration could provide insights into critical Cold War decisions on issues ranging from the Cuban missile crisis to Vietnam.

Yet the Kennedy family, led by Robert’s widow, Ethel, has rarely permitted even limited access to the papers. Their expansive control of the RFK archive, which extends to dozens of Pentagon, State Department, and CIA documents, stems from a controversial agreement reached with the National Archives following Robert Kennedy’s assassination in 1968.

Numerous government archivists and historians maintain the family should never have been granted oversight of the official documents — only the files containing private information, such as correspondence with Jacqueline Kennedy Onassis and a collection of materials involving famous family acquaintances like Frank Sinatra.

“It was inappropriate [for the National Archives] to allow it,” said William J. Leonard, who recently retired as chief overseer of the government classification system. “Classified information by definition is information that is under the government’s control.”

Put another way, “Ethel has been given control of documents that she couldn’t even legally read because she didn’t have a security clearance,” said a former National Archives official who had the authority to handle top secret information regarding the RFK papers.

The Globe first reported in January 2011 that most scholars have been unable to get access to the documents. But the index reveals for the first time an overview of the contents of the collection and the fact that most of the documents are not personal papers.

Representatives of the Kennedy family declined requests to discuss the issue in detail. Matthew Maxwell Taylor Kennedy, who has handled the issue on behalf of his mother, said in an e-mail that the family was deferring questions to Joseph E. Hakim, a business executive who formerly oversaw some of the family’s financial holdings.

“I know he is working hard with the National Archives to figure out a way to release all of the papers,” Max Kennedy said.

Hakim did not respond to several telephone messages and e-mails.

According to a person who has been closely consulted by the family on the issue, the government’s mishandling of the papers began when Kennedy’s office was packed up in the summer of 1968 and the contents sent to the National Archives for storage.

“RFK had access to classified documents and who knows what he had in his offices when he died,” said the person, who spoke to the Globe on the condition of anonymity, for fear of upsetting the family.

Several years later the National Archives and RFK’s heirs reached what Thomas J. Putnam, the director of the John F. Kennedy Library and Museum in Columbia Point, described as a “deposit” agreement.

In the legal memorandum, he said, the family agreed to keep the papers in the JFK Library but was given the right to review any access to them. The family also agreed that it would sign a deed granting the National Archives full control of most, if not all, of the documents. But there was no deadline set for the deed, and despite the library’s efforts, negotiations to secure one have started and stalled repeatedly over the decades.

“The family should never have had ownership of the classified documents to begin with,” said the family confidant. The deal with the National Archives to house the papers, crafted in the emotional aftermath of the assassination, “had errors that led to the family feeling ownership. . . . The family holds dear the professional papers of both husband and father.”

The Kennedy family has said it granted access to the papers to a few historians, but library officials maintain no one has seen them all — out of concern for the family’s privacy or because so many files were stamped secret.

Even the author hand-picked by Ethel Kennedy to write a comprehensive biography of her husband — former Kennedy White House aide Arthur M. Schlesinger — was granted limited access, according to private correspondence recently reviewed by the Globe.

“I told her that there would be no direct quotes from the papers without her permission,” Burke Marshall, who ran the Civil Rights Division at RFK’s Justice Department, wrote to Schlesinger on Mrs. Kennedy’s behalf in February 1969.

In his private notes, Schlesinger himself expressed frustration in 1985 that the files were not fully released.

Papers from other chapters of Robert Kennedy’s public life — including when he served as his brother’s campaign manager; his efforts in the Justice Department to combat organized crime; and his three years as US senator from New York — have been released by the library with the family’s consent.

The withheld files are broken into two categories, according to the nearly 40-page index, whose authenticity the Globe verified with a former library official who worked directly with the collection. About half make up the attorney general’s so-called “classified” file and the rest are labeled the attorney general’s “confidential” file.

Both series of files document Kennedy’s broad portfolio as the president’s most trusted adviser, including in foreign policy. That was a distinct departure from previous attorneys general, who were responsible almost solely for domestic law enforcement.