John Reid has won a famous Whitehall victory. The splitting of the Home Office has been despite the strong opposition of much of the Civil Service establishment, as well as most of his recent predecessors as Home Secretary. Charles Clarke described it as an “irresponsible decision”.

The main doubts are less about the shake-up of counter-terrorism planning and coordination in the Home Office, and more about the consequences for the criminal justice system of the creation of a justice ministry out of the Department for Constitutional Affairs. Mr Reid has won because the terrorism card is invariably a winner in Whitehall debate, especially with Tony Blair. The Treasury has gone along — with Gordon Brown supporting his old Scottish rival — mainly because of the assurance that the changes will not involve extra public spending. But there is still a lot of tricky bargaining over the allocation of budgets after the transfer of prisons and probation (the National Offender Management Service) to the justice ministry.

Mr Reid can sound like a revivalist preacher in urging urgent reorganisation. The intentions, capabilities and numbers of potential terrorists are worryingly large: 200 groups, 1,600 identified individuals and 30 or more plots to kill people (100 plus, according to Mr Reid). The missing link, in his view, is strategic coordination, research, planning and information. Hence the new Office for Security and Counter-Terrorism in the Home Office, eventually 300 to 400 strong, which will be accountable through a new ministerial committee.

This will supplement the independent work of the main intelligence agencies and the assessment role of the Joint Intelligence Committee. That is sensible. The agencies can feed into the counter-terrorism office without risking the political embrace which compromised some intelligence before the Iraq war. But does all this require the break-up of the Home Office? It has already lost several big functions in shake-ups since 2001. Mr Clarke and others fear that the drive behind reforms of criminal justice will be lost. Problems of coordination between immigration and prisons which cost Mr Clarke his job last May could be exacerbated by the change. Mr Reid’s view is that the absence of coherent coordination now makes the case for the split. But this is not persuasive, and has not persuaded many well-informed current and former ministers and officials. Moreover, Lord Kingsland, the Conservative Shadow Lord Chancellor, thought there was “a serious conflict of interest” in having sentencing and prisons in the same department.

There are several loose ends. The leadership of the justice ministry — currently in the hands of Lord Falconer of Thoroton — is, as Mr Reid said, likely to move to the Commons after a “transitional period”. That means when we have a new prime minister. There is no legal reason why the Lord Chancellor cannot be an MP, however much it will infuriate peers to have just one Cabinet minister in the Lords. Moreover, a new anomaly has been created. It makes no sense for constitutional affairs, including electoral reform, to be within a justice ministry. So expect further changes when Gordon Brown takes over.

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