A controversial proposal by the Government to extend pre-charge detention for terror suspects to up to 42 days could undermine the help that Muslim groups are giving police, according to the Home Office’s official assessment of the measure.

The groups also said that a planned new offence, making it illegal to collect information on members of the Armed Forces likely to be useful to a terrorist, would reinforce concerns that they were not sure what they were allowed to talk about.

The assessment, published alongside the Counter Terrorism Bill yesterday, said that there was a belief among the Muslim community that it was being discriminated against and that this may continue under the new law.

“Muslim community representatives expressed a concern that this may lead to increased reluctance among their communities to provide vital co-operation and assistance to the police and security services,” the equality impact assessment on the Bill said. The Bill’s key proposal to increase from 28 days to up to 42 days the time police can hold terror suspects without charge came under a barrage of criticism from opposition MPs and civil liberties groups.

Jacqui Smith, the Home Secretary, said that the plan to extend pre-charge detention, which is expected to run into trouble with Labour backbenchers, would come into force only in “exceptional operational circumstances” such as multiple terror plots, the need to interview suspects abroad and retrieve large amounts of information from computer disks. Powers to impose the 42-day limit would be kept in reserve and could only be brought in temporarily. Under the plan, the Home Secretary will be able immediately to extend the limit to 42 days if a joint report by a chief constable and the Director of Public Prosecutions backs the move. Parliament will have to approve the extension within 30 days but if either House votes against the move, the power comes to an end at midnight on the day of the debate.

The limit will be available to police for two months at any one time unless it is renewed. Individual detentions over 28 days will be extended every seven days on the approval of a judge. A suspect could be held for 42 days even if Parliament eventually refused permission for an extension beyond 28 days. If the Home Secretary decided on an extension towards the end of the existing 28-day limit, Parliament would not have to approve it for 30 days. In such circumstances a suspect could have been charged or released by the time a vote was due. The Government has insisted that even if Parliament were to reject an extension to 42 days, a person would still have been lawfully held. David Davis, Shadow Home Secretary, said the Government had produced no evidence to justify extending pre-charge detention.

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