James and The Anglican were again embroiled in controversy in 1964 when James was fined fifty pounds for publishing offensive publications -- the infamous Oz magazine.

While the vast majority of Australians initially supported the conscription move, a vocal minority opposed the introduction of conscription and any Australian involvement in the Vietnam War. Francis James, opposed involvement in the Vietnam War from the early days. He successfully used The Anglican as a platform to conduct his opposition to Australian involvement in the Vietnam War throughout the 1960's. From 1962 to 1969 he addressed over two hundred public meetings and wrote dozens of articles opposing the Vietnamese War on moral and logistical grounds.

James became involved with anti-war groups who generally sought to use legal tactics aimed at influencing public opinion and thus reversing government policies on the war within the framework of the Australian parliamentary systems and existing social institutions. These groups included the Association for International Cooperation and Disarmament (AICD), the Ex Services Human Rights Association of Australia (ESHRAA) and the Liberal Reform Group (LRG). James's opposition to the Vietnam War ultimately saw him stand as a candidate for the Liberal Reform Group in the November 1966 election. Though unsuccessful, organisations such as the Liberal Reform Group highlighted the growing unrest in middle class Australia to continuing involvement in the Vietnam War.

In 1967, James was involved in a controversy over sending money to North Vietnamese aid organisations. James campaigned against the Defence Force Protection Act, which made it illegal to send money to certain named organisations including the Communist Party of North Vietnam and the National Liberation Fronts of North and South Vietnam. The furore over Australians sending money to North Vietnam had been sparked by a decision by the Monash University Labor Club to collect aid for the National Liberation Front (NLF). Many Australians were outraged that Australian students were sending aid to an enemy force and demanded government action. In August 1967, Francis James took part in a debate at the Melbourne University Union. The debate topic was 'that every Australian has the democratic right to send aid to the NLF'. James argued the affirmative case based on the legal doctrine that there was no law in existence that prevented people from sending whatever aid they wished. Accordingly, they enjoyed the democratic right to do so. The motion was carried 850 to 150. The Australian Broadcasting Commission obtained permission to record the debate and broadcast an edited version on 9 August 1967. By 12 August 1967, media speculation had resulted in the Attorney-General, Nigel Bowen, making a statement that he was looking into the activities of the Monash students with a view to laying criminal charges. On 16 August 1967, Prime Minister Harold Holt was asked in the House of Representatives about the 'published decision of the Monash University Labor Party to help raise funds for the Vietcong, therefore assisting in the killing of Australian soldiers'.

By 20 August, the Red Cross in Melbourne revealed that it had contributed over $650,000 of medical and other supplies to North Vietnam during the past two years. Additionally it had promised 17,000 blood donations to Hanoi. On 21 August, the ANZ Bank, banker for The Anglican, informed James that no more overseas drafts would be supplied unless documentation regarding the transaction was produced. By 25 August 1967, because of the radio broadcast, James had been sent over $30,000 for the cause. In accordance with the wishes of the donors, James sent $33,877 through ordinary banking channels, to the International Red Cross, through the relief agencies of the Holy See and the World Council of Churches. In the case of money he was asked to send to the NLF, it was sent wholly in the form of credits with established pharmaceutical or surgical companies.

James made a second visit to North Vietnam in 1968 somewhere between the Tet Offensive in late January and April. According to James the purpose of the visit was trade. During the visit, he met with a Belgian priest, Jean Potelle, and a French businessman who had been a fellow prisoner of war. Unusually for James, he revealed few details of this trip publicly although he gave a lecture to members of the Australian Institute of International Affairs. James's anti war activities ended abruptly in 1969 when he was imprisoned by the Chinese on suspicion of spying. By the time that James was released in January 1973, Australian involvement in Vietnam had ended.

Francis James was released in January 1973 after three years of imprisonment. This release had been secured by extensive negotiations between then Prime Minister, Gough Whitlam, and Chinese officials. The Chinese government stated that they were deporting James because he had been found guilty of espionage. James wrote a series of articles about his imprisonment, which were published by the Sydney Morning Herald in January and February of that year. In 1986, James was 'rehabilitated' by the Chinese government. Francis James died in 1992 after a short illness.

Francis James had an enduring interest in international affairs. He held various positions in a range of organisations including councillor of the Royal Australian Institute of Public Affairs from 1954-1960 and Secretary of the Primate's Commission on International Affairs. In late 1956, James accompanied a group of Anglican clergymen led by the Primate of Australia Dr A Mowll to Fukien province in China. The group included Marcus Loane, Bishop Co-Adjutor of Sydney. Dr Mowll was returning to China for the first time in almost a decade and compared the conditions before and after 'Liberation'. Despite his misgivings about the progress made in China, the visit to China prompted the Australian Security Intelligence Organisation (ASIO) to open a file on James's activities. Documents available from the period 1956 to 1960 chronicled James's involvement with groups such as the Australia China Society.

James was an enigmatic figure in life and death. In 1992 when delivering the eulogy at James's funeral, Sir Marcus Loane, the former Archbishop of Sydney, described Francis James as a born entertainer, a complete extrovert and a real mischief-maker who revelled in controversy. His friends were everywhere - politicians, journalists, churchmen and pilots. Barrowclough compared James to Graham Greene saying that like Greene, James was a man of secrecy, ambiguity and paradox, a person who believed deeply in the Christian faith but declared his support for Asian communist governments. Phillip Knightley often wondered if James was a spy, a view shared by other journalists who had known James. Bob Ellis recounted some of James's clownish interventions into history including flying to Hanoi during the Vietnam War and feigning an assassination attempt (with an egg timer) on then United States President, L. B. Johnson. Peter Edwards compared James to a 'medieval jester…who often says the truth…in a way that serious counsellors at the court were not allowed to say'. James had once remarked to Anna Murdoch that 'no one will ever know the real Francis James', perhaps an attempt by James to maintain copyright on his life.