Australia’s top spy boss lobbied his counterpart in Washington to keep secret an investigation of anonymous phone calls to the US embassy in Canberra around the time of President John F Kennedy’s assassination.

Formerly secret documents declassified by the Trump administration show the then-head of ASIO, Sir Charles Spry, wrote to CIA director Richard Helms in October 1968 recommending against public disclosure of the investigation.

A document referring to the CIA probe of a Canberra link to the plot against JFK in 1963 was held by the Warren Commission, the inquiry ordered by Mr Kennedy’s successor Lyndon Johnson.

“Sir Charles’ letter to you recommends against declassification of the Warren Commission document … which refers to our investigation of anonymous phone calls to the Canberra Embassy before and after the assassination of President Kennedy,” a memo to Mr Helms in November 1968 said.

Its author, CIA Far East Division chief William Nelson, said he considered “the points made by Sir Charles in his letter to be valid and accordingly recommend declassification … in the foreseeable future”.

Days later, Mr Helms wrote to Sir Charles, reassuring him that there was “not, at the present time, any intention to release [the document]”.

The CIA had consulted with ASIO months earlier in what Mr Helms said was “anticipation of further pressure for the release of Warren Commission papers, a pressure which has not materialised”.

“Should the question be raised at some future time, the points made by you in your letter provide every reason to keep the document out of the public domain,” Mr Helms said in his letter.

JFK’s murder has been the subject of unending conspiracy theories despite official bodies, including the Warren Commission, deeming it the work of lone gunman Lee Harvey Oswald.

JFK’s nephew, Robert F Kennedy Jr, now serving with the Trump administration as secretary of health and human services, has alleged CIA involvement in his uncle’s death.

On the first release of JFK investigation documents in January, Mr Kennedy said there had been a “60-year strategy of lies and secrecy, disinformation, censorship, and defamation employed by intel officials to obscure and suppress troubling facts about JFK’s assassination”.

Robert F Kennedy Jr has claimed his uncle’s 1963 assassination was shrouded in “secrecy and lies” by intelligence officials. (Reuters: Nathan Howard)

CIA secret recordings, a mystery car, and ALP MPs

Among the ream of documents released today was a secret CIA report in December 1963 from its then-Melbourne director regarding “preliminary checks on recorded conversations”.

It said there was “no trace” on a 1952 dark blue Buick “belonging [to] Soviet or bloc installation [in Canberra] or Sydney”.

There was “no license [sic] plate identical to[the] one mentioned” but checks were done on “NSW variants”, belonging to three men.

The cable also reveals the CIA’s interest in “information on the Polish driver connected with the Russian diplomatic establishment in Australia”.

It made reference to Labor parliamentarians but the meaning was unclear: “Frasers mentioned same ref are ALP MPs.”

It also revealed the CIA was keeping tabs on an Indonesian diplomat in Canberra, Willy Sastranegara, in regard to any dealings with the US Cold War enemy, the Soviet Union.

Mr Sastranegara had arrived in Canberra in 1959 as a representative of the left-wing anti-colonialist government of Indonesian president Sukarno.

“[Indonesia] first [secretary] possibly IDW R. Willy Sastranegara has moustache; Russian capability not known to square; not noticeably close to [Soviets in Canberra].”

The CIA had arranged to “trace any further calls made”, the report said.