Jeffrey has been criticised by the Public Accounts Committee chairman Edward Leigh for prioritizing the renovating of leisure facilities over the "unacceptable housing" conditions for troops and their families.^[4] The paper said 19,000 service homes were in disrepair, half of all single accommodation was "below par" and that some servicemen would have to wait 20 years for improvements.^[4] Edward Leigh said: "...you (Bill Jeffrey) have cut £13.5 million of essential work out of regional prime contracts, but you have obliged the same contractors to do £45 million on other projects, including resurfacing tennis courts and building all-weather pitches.^[5]

As director-general of the Immigration and Nationality Directorate Jeffrey formulated a concerted policy of risk-taking by immigration staff who were asked when processing non-European Union migrants applying to work, study or marry to attempt, where possible, to make positive (permissive) judgments where it was not certain that applications could be denied.^[6] He communicated this policy, applying to hundreds of thousands of cases, in a note to Beverley Hughes, minister of state for citizenship and immigration. Hughes was later forced to resign for misleading MPs about whether she had been warned of the likely threat of Romanian and Bulgarian crime gangs taking advantage of the UK opening its borders to those seeking work from eastern Europe. This Whitehall correspondence, which was illegally withheld by the Home Office for four years, reveals an official policy to grant applications rather than to refuse them, thus fast-tracking over 300,000 applications with minimal checks. According to Times reporters, a number of serious criminals were admitted, including members of the Taliban.^[6]