The Counter-Terrorism Bill is making its way through Parliament
MPs have rejected a move by peers to allow phone tap evidence to be used "in exceptional circumstances" in inquests presided over by a High Court Judge.
The move was intended to allow inquests to take place even though sensitive security information was involved.
MPs voted by 284 to 220 to reject an amendment to the Counter-Terrorism Bill, a government majority of 64.
They have also overturned a move calling for new guidelines on destroying innocent people's DNA.
The Conservatives backed a Lords amendment which would change guidelines for police on when to authorise destruction of an innocent person's DNA.
Shadow Home Office minister Damian Green said "draconian" rules practically ruled out the chance of anyone ever being able to have their fingerprints and DNA deleted from national databases.
DNA and fingerprints
Home Office guidance meant senior police officers were only able to use their discretion in the most exceptional of cases, he said.
The Lords amendment would have made it easier for a person to get their records deleted by establishing a national procedure and putting an obligation on police to explain why they refused a deletion request, he added.
But Home Office minister Vernon Coaker said there was "strong and convincing evidence to support the existing approach", as the DNA profiles helped solve serious crime.
The rights of individuals who have their DNA and fingerprints taken were already contained in guidance, he argued.
But he added: "I do agree that there is work to be done to publicise these rights more widely."
Mr Coaker said there was a current review of the Police and Criminal Evidence Act guidelines. He wanted to ensure "greater consistency across the country".
The Lords amendment was overturned by 277 votes to 209, a government majority 68.
On phone tap evidence, Mr Coaker told MPs: "The fundamental difficulty with the amendment and where the disagreement has come forward is that inquests must be held with a jury in certain circumstances and that juries are finders of fact.
"The Lords amendment would mean sensitive material would have to be disclosed to the jury for the inquest to proceed and this risks it then being disclosed."
He said the matter would best be dealt with in the forthcoming Coroner's Bill.
But Mr Green expressed concern that the issue was being "pushed back" into another piece of legislation, as there were "urgent present cases" where inquests could not happen because this particular law was not in place.
And Labour MP Jeremy Corbyn said the Lords amendment offered a "far better" approach.
He told MPs: "It is too easy for the agents of the state, be they the armed forces or the police or social services or health service, to say 'well, hang on there's something very very peculiar and very very sensitive about this' and go to the judge and say 'I'd rather this was not disclosed.'"
Home Secretary Jacqui Smith has already withdrawn the Counter-Terrorism Bill's most controversial clauses - which would have extended pre-charge detention of terrorist suspects from 28 days to 42 - after they were overwhelmingly rejected by peers in October.