Mr Lewis, who was removed by Michael Howard, the Home Secretary, last October, said that without that, ministerial accountability is "seriously undermined" and agencies "will increasingly be led by emasculated political poodles".
Speaking at a Campaign for Freedom of Information conference in London, Mr Lewis said that ministers are left free to impose "half baked" policies or set the agencies "wholly unrealistic" performance targets.
Inquiry recommendations following the escapes from Whitemoor and Parkhurst prisons would cost "millions of pounds", he said. But the public had a right to know that management believed that was not good value for money.
Without the ability for agencies to speak out, ministers would to categorise all difficult issues as "operational", thus placing blame on the agency. The result would be to "give ministers authority without responsibility; and agencies responsibility without authority".
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