On the 50th anniversary of Jung's death it is time to put accusations of him collaborating with the Nazis to rest

Jung's relationship with Freud was ambivalent from the start. First contact was made in 1906, when Jung wrote about his word association tests, realising that they provided evidence for Freud's theory of repression. Freud immediately and enthusiastically wrote back. But Jung hesitated. It took him several months to write again.

They met a year later and then it was friendship at first sight. The two talked non-stop for 13 hours. Freud called Jung "the ablest helper to have joined me thus far", and spoke of how Jung would be good for psychoanalysis as he was a respected scientist and a protestant – a dark observation that was to haunt Jung three decades later when the Nazis came to power.

For now, different tensions persisted. A request Jung made highlights one axis of difficulty: "Let me enjoy your friendship not as one between equals but as that of father and son," he wrote. The originator of the Oedipus situation, in which murderous undertones supposedly exist between a father and a son, was alarmed. Freud did anoint Jung his "son and heir", but he also experienced a series of neurotic episodes revealing the fear that Jung was a threat too.

One such incident occurred when they travelled together to America in 1909. Conversation turned to the subject of the mummified corpses found in peat bogs, which prompted Freud to accuse Jung of wanting him dead. He then fainted. A similar thing happened again a while later.

A different sign of conflict came when Jung asked Freud what he made of parapsychology. Sigmund was a complete sceptic: occult phenomena were to him a "black tide of mud". But as they were sitting talking, Jung's diaphragm began to feel hot. Suddenly, a bookcase in the room cracked loudly and they both jumped up. "There, that is an example of a so-called catalytic exteriorisation phenomenon," Jung retorted – referring to his theory that the uncanny could be projections of internal strife. "Bosh!" Freud retorted, before Jung predicted that there would be another crack, which there was.

All in all, from early on, Jung was nagged by the thought that Freud placed his personal authority above the quest for truth. And behind that lay deep theoretical differences between the two.

Jung considered Freud too reductionist. He could not accept that the main drive in human life is sexual. Instead, he defined libido more broadly as psychic energy or life force, of which sexuality is just one manifestation. As to the Oedipus complex, Jung came to believe that the tie between a child and its mother was not based upon latent incestuous passion, but stemmed from the fact that the mother was the primary provider of love and care. Jung had anticipated the attachment theory of John Bowlby, which has subsequently been widely confirmed.

Jung also believed that the contents of the unconscious are not restricted to repressed material. Rather, the unconscious resources an individual's life. A human person is built up of layers. The conscious aspect is the psychosomatic whole that comprises the body and cognisant mental life. Beneath that lies a personal unconscious, a supply of material from the life of the individual. And beneath that lies a collective unconscious that is inherited. Jung believed he had objective evidence for this common heritage from his studies of schizophrenics, who apparently spoke of images and symbols they could not have discovered in their reading, say, or culturally.

It is a contentious proposition to which we will return. For now, it's worth noting that again Jung anticipates post-Freudian theories, this time about the nature of the unconscious. In his recent book, The Social Animal, David Brooks observes that 21st century sciences are showing how the unconscious parts of the mind "are not dark caverns of repressed sexual urges." Jung wrote precisely that 100 years ago, and neuroscientists, psychologists and economists of today might find parts of Jung a highly suggestive read.

For Freud, Jung was becoming a highly uncomfortable read, and by 1913 their friendship was at an end. Jung maintained his respect for Freud though: when he wrote Freud's obituary in 1939, he observed that Freud's work had "touched nearly every sphere of contemporary intellectual life". However, the betrayal that Freud felt has arguably spoiled relationships between the two schools of psychodynamic thought to this day. I was recently speaking with a Freudian analyst who quite casually referred to Jung as a womaniser and Nazi. We considered the first accusation last week. Now, we should consider the anti-Semitic charge.

The evidence is carefully weighed in Deirdre Bair's biography and, in retrospect, Jung could be accused of making mistakes during the 1930s. However, other actions he took clearly rescue his reputation.

The accusation that he was a Nazi fellow traveller stem from evidence such as a magazine article he had written 1918. Jung drew distinctions between Jewish and German psyches to illustrate the variety of heritable elements of the collective unconscious. When Aryans reread the article in the 1930s, they distorted it out of all proportion. Further, they glossed over another observation, that the German psyche had "barbarian" tendencies, Jung's reflection on the 1914-18 war. They also missed his main point that the unconscious should be taken very seriously. It can drive the death of millions.

Jung is also accused of complying with the Nazi authorities, in particular with Matthias Göring, the man who became the leader of organised psychotherapy in Germany, not least because he was the cousin of Hermann Göring. In fact, Matthias put Jung's name to pro-Nazi statements without Jung's knowledge.

Jung was furious, not least because he was actually fighting to keep German psychotherapy open to Jewish individuals. And that was not all. Bair reveals that Jung was involved in two plots to oust Hitler, essentially by having a leading physician declare the Führer mad. Both came to nothing.

It has also come to light that Jung operated as a spy for the OSS (the predecessor to the CIA). He was called "Agent 488" and his handler, Allen W. Dulles, later remarked: "Nobody will probably ever know how much Prof Jung contributed to the allied cause during the war."

After the war, Rabbi Leo Baeck, a survivor of the Theresienstadt concentration camp, confronted his friend about his involvement with the Nazis. Jung admitted failings, though perhaps also had the chance to tell a fuller story. Baeck and he were fully reconciled. Fifty years after Jung's death, the anniversary that falls today, it is time that casual Nazi accusations ceased too.