Equally difficult, Kelley was appointed at the worst possible time. The collapse of President Richard Nixon's notorious Watergate cover-up in 1973-74 threw harsh and revealing light on years of abuse of power by the US intelligence community. Both the FBI and, in some ways more seriously, the Central Intelligence Agency, in charge of foreign security, were gravely compromised.
Finally, the timing and circumstances of Kelley's appointment made his efforts to end these abuses and reform the FBI even harder. L. Patrick Gray III, who had been made acting director on Hoover's death, was forced to resign in 1973 when it emerged he had destroyed sensitive documents relating to the Watergate conspiracy.
Eventually Nixon's attorney general John Mitchell was jailed, the CIA director Richard Helms brought under suspicion and the president himself forced into the unprecedented step of resigning - all because of the ramifications of what Nixon's press secretary had at first tried to dismiss as "a third- rate burglary".
Clarence Kelley, nominated by Nixon over 26 other candidates, had plenty of experience of both third-rate and first-rate burglaries, and indeed crime and political corruption of every kind. Originally an FBI man, he had left in 1961 to become chief of police in his home town, Kansas City, Missouri, one of the most notoriously corrupt cities in America.
When Kelley was growing up there in the 1920s and 1930s, Missouri was still run by the political machine controlled by the Pendergast family since the 1870s. But Kelley, the son of an electrical worker, had an honest, hardworking upbringing in the best American tradition. He was throughout his life an active Christian with the Disciples of Christ and prominent in charity work. He graduated from the University of Kansas in 1936, and took a law degree from Kansas City Law School in 1940.
Such was his idealism, that a speech by the head of the Kansas City FBI office at his graduation ceremony inspired him to join the Bureau, which he did in the following year.
During the next 20 years he served in ten cities across the United States, apart from a break between 1943 and 1946 when he was drafted into the US Navy. On demobilisation, he briefly worked at the FBI Academy in Virginia, where the dogged, incorruptible traditions of the bureau were first instilled. But his time spent running FBI offices in Birmingham, Alabama, and Memphis, Tennessee in the 1950s, when the civil rights movement was starting its epic progress, was more significant. J. Edgar Hoover, who regarded the whole civil rights campaign as part of the international Communist conspiracy, did nothing to encourage it. Indeed, he despised its leader, Martin Luther King, and illegally tapped his phone, along with those of hundreds of other liberal activists.
Though Kelley may not have shared his boss's paranoia, he had the same racial prejudices of most white Americans of his generation. This became more apparent when he left the Bureau in 1961 to become chief of police in Kansas City. Corruption, as usual, was rife, with his immediate predecessor and four department heads facing indictment for dishonesty.
More serious, in a city where a fifth of the population was African-American, only five per cent of police officers were black. It was hard for a man of Kelley's background and experience in the lily-white FBI to balance the aspirations of the city's blacks against the bigoted fears of the white working class from where the comparatively poorly-paid policemen came.
Civil rights activities, which increased in the 1960s, exploded in April 1968 when King was assassinated. Angry, grief-stricken demonstrators in Kansas City, mostly women and children, were dispersed by batons and tear gas. This led to real rioting, during which six unarmed blacks were killed. Kelley refused to apologise and no one was brought to book. Though the proportion of black police officers doubled during his 12 years as chief, and crime was cut by a quarter, his reputation was permanently stained by this incident.
Back at the FBI, Kelley had to weather the storm of protest stirred up by the Watergate revelations, and not only hold the Bureau together but try to transform it into something more appropriate to changed times. The kind of managerial and technical reforms he had accomplished at the Kansas City police department, which Hoover in old age had prevented at the FBI, were repeated to make the Bureau into a more efficient investigative organisation.
Computers, resisted for years because of Hoover's fixation with files, were introduced. Fear of what Hoover's famous files might contain had stopped successive presidents from replacing him, and Congress from criticising him. Now it was revealed that they had consisted mostly of newspaper clippings. Recruiting was also transformed. Agents, who until the 1970s had been almost entirely white men, began increasingly to include blacks, Hispanics and women.
But the real problem remained redefining the role of the FBI and keeping it under proper public control. At his confirmation hearings Kelley had helped win endorsement by promising to provide Congress with itemised FBI financial accounts - something Hoover would have rejected with contempt.
Yet political rather than financial accountability was what really mattered, and here Kelley had only limited success. Though he assured Congress that illegal FBI burglaries had ceased in 1966, he later had to admit they had continued right up to 1973. In 1976 he ordered that all FBI open operations, more than 21,000, be reviewed and halted unless they showed real evidence of crime or threat to national security.
For despite Hoover's legacy, there were enough agents within the Bureau to back reform, and on appointment Kelley had been welcomed as an FBI man and not some outsider. Moreover, some of the early criticism about the way the intelligence services were operating had come covertly from within the CIA and FBI, or openly from former officers.
But this opportunity was largely squandered. Though the ghost of internal Communism was finally exorcised, and attention focused on real dangers like organised crime, and white-collar crime, in the wake of Watergate the FBI had for the first time become a political football.
This finally brought Clarence Kelley down. Critics pointed to the fact that staff at FBI headquarters had grown from 475, when he took over, to more than 900 by 1977. Worse, when it was discovered that Kelley, like Hoover, had used FBI staff to improve his home, Jimmy Carter, campaigning for president in 1976, made an issue of it.
Kelley repaid the trivial sum of less then $400. But President Carter promised not to reappoint him at the end of his term. Rather than face this, Kelley retired in 1978 and Carter appointed Judge William H. Webster in his place.
Clarence Marion Kelley, police officer: born Kansas City, Missouri 24 October 1911; Director of the Federal Bureau of Investigation 1973-78; married 1940 Ruby Pickett (died 1975; one son, one daughter), 1976 Shirley Ann Dyckes; died Kansas City 5 August 1997.