Little-noticed provisions in last month's Counter-Terrorism Bill would allow Jacqui Smith to block the summoning of a jury and parachute in her own choice of coroner if she deems it to be in the interests of national security or the UK's relationship with another country or "otherwise in the public interest".

Although it is included in a bill to tackle the threat of terror, the new powers are not explicitly restricted to terrorism cases and could in theory be applied to cases of deaths where no link with violent extremism is suspected.

The Joint Committee on Human Rights warned that the measures could be invoked to limit scrutiny of deaths of British servicemen killed by US "friendly fire" in Iraq or the shooting of Jean Charles de Menezes, who was mistaken by police for a suicide bomber.

The Committee branded the inquest plans "astonishing", especially as they were introduced into the Bill at a late stage with no time for consultation or pre-legislative scrutiny.

Andrew Dismore MP, the Labour chair of the Committee, said: "We are seriously alarmed at the prospect that under these provisions, inquests into the deaths occurring in circumstances like that of Jean Charles de Menezes, or British servicemen killed by US forces in Iraq, could be held by a coroner appointed by the Secretary of State sitting without a jury.

"Inquests must be, and be seen to be, totally independent and in public to secure accountability, with involvement of the next of kin to protect their legitimate interests.

"When someone dies in distressing, high-profile circumstances their family need to see and feel that justice is being done, and where state authorities are involved there is a national interest in accountability as well."

The report warned that the new measures may breach the European Convention on Human Rights, to which the UK is a signatory.

"On first inspection we find this an astonishing provision with the most serious implications for the UK's ability to comply with the positive obligation in Article 2 (of the) ECHR to provide an adequate and effective investigation where an individual has been killed as a result of the use of force, particularly where the death is the result of the use of force by state agents," it said.