At least 22 organisations - covering contracts worth £1.8 billion - have been required to sign the clauses as part of their involvement with programmes getting the unemployed into work, The Times reported.
Officials at the Department for Work and Pensions (DWP) denied they were "gagging clauses" intended to prevent criticism of ministers or their policies, insisting they were just "standard procedure".
However a spokesman confirmed that the contracts did include references to ensure both parties "understand how to interact with each other and protect their best interests".
The signatories to contracts must undertake to "pay the utmost regard to the standing and reputation" of the Work and Pensions Secretary, the newspaper reported, adding that they must "not do anything which may attract adverse publicity" to her, damage her reputation, or harm the public's confidence in her.
A DWP spokesperson said: "It's completely untrue to suggest that organisations are banned from criticising Universal Credit. As with all arrangements like this, they include a reference which enables both parties to understand how to interact with each other and protect their best interests.
"This is in place to safeguard any commercial sensitive information for both government and the organisation involved."
The disclosure comes after Ms McVey confirmed that some people would be worse off as a result of the introduction of UC, saying the Government had taken some "tough decisions".
Former prime minister Sir John Major called for a rethink of the planned roll-out of UC to more than two million claimants of existing benefits, warning the Government risked a poll tax-style backlash if the policy was seen as unfair.
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