The head of MI6 has claimed that national security has been so badly damaged by the leaking of NSA files that Britain’s adversaries have been “rubbing their hands with glee” and al-Qaida is “lapping it up”.

But despite the robust language from Sir John Sawers, in the first joint public hearing by the heads of Britain’s three intelligence agencies, there were also signs that some parliamentarians were unaware of the extent of domestic spy agencies’ co-operation with foreign intelligence agencies, such as the relationship GCHQ has with the US National Security Agency.

Sawers warned that the leaks by Edward Snowden had damaged national security by alerting “targets and adversaries” to Britain’s capabilities.

Speaking to MPs and peers on parliament’s intelligence and security committee (ISC), Sawers said: “The leaks from Snowden have been very damaging. They have put our operations at risk. It is clear that our adversaries are rubbing their hands with glee, al-Qaida is lapping it up and national security has suffered as a consequence.”

Sir Malcolm Rifkind, the former Tory foreign secretary who chairs the ISC, immediately challenged Sawers to justify his remarks, but the spy chief did not provide additional details.

“I don’t want to repeat what my colleagues have said,” Sawers replied, in reference to a warning by the director of GCHQ, Sir Iain Lobban, that Britain’s “fragile mosaic of strategic capabilities” was in a weaker position since the first Snowden leaks in June.

The chief of MI6 then added: “They [the other intelligence chiefs] have very clearly set out just how the alerting of targets and adversaries to our capabilities means that it becomes more difficult to acquire the intelligence that this country needs.”

Asked by Rifkind whether he had more hard evidence than that outlined by Lobban, who claimed terrorists had been looking at the media reports and had changed their plans, the GCHQ director intervened over Sawers to say: “Not in this public forum, chairman.”

One member of the committee, Mark Field, voiced concern that the ISC had not been aware of all the “intricacies” in the spy programmes revealed by newspapers such as the Guardian and asked for a comprehensive update of all collaboration with foreign agencies in a closed session, which Lobban agreed to.

Lobban said that the intelligence agencies had embarked on an “active debate” about greater transparency. Asked by Rifkind whether the line between secrecy and openness could be redrawn without endangering the battle against terrorism, the GCHQ head said: “I actually think that has been quite an active debate even before the recent revelations.

“I think when the committee produces your own report – and you seek to produce it in as unredacted a form as possible – clearly with the situation we are in we are actively considering that with government.”

The exchanges between Sawers and Rifkind came after the GCHQ director issued the most detailed account during the ISC hearing of the impact of the Snowden leaks.

Lobban said that the leaking of NSA files, which include documents on the work of GCHQ, would lead to an inexorable darkening of intelligence information about terrorists, organised criminals and paedophiles.

Lobban said: “Sigint [signals intelligence, sources and methods] successes over decades, going back to the second world war and beyond, depend upon our intelligence targets being at best unaware or at best uncertain of our successes. So if you think what happens if Sigint are revealed. It can be a sudden darkening. More often it is gradual but it is inexorable.

“So what we have seen over the last five months is near daily discussion among our targets and I will bring out some, I will give you an example.

“We have seen terrorist groups in the Middle East, in Afghanistan and elsewhere in South Asia discussing the revelations in specific terms – in terms of the communications packages they use, the communications packages they wish to move to.

“We have intelligence on, we have actually seen chat around specific terrorist groups, including closer to home, discussing how to avoid what they now perceive to be vulnerable communications methods or how to select communications which they now perceive not to be exploitable. I am not going to compound the damage by being specific in public. I am very happy to be very, very specific in private.”

Rifkind asked Lobban whether he could state that the changes in methods by terrorists were a direct result of the media reports on the Snowden leaks.

“Absolutely,” he replied. “It is a direct consequence; I can say that explicitly. The cumulative effect of the media coverage, global media coverage, will make the job we have far, far harder for years to come.

“There is a fragile mosaic of strategic capabilities, which allow us to discover, to process, to investigate and then to take action. That uncovers terrorist cells, it reveals people shipping secrets or expertise or materials to do with chemical, biological or nuclear around the world.

“It allows us to reveal the identities of those involved in online sexual exploitation of children. Those people are very active users of encryption and of anonymisation tools. That mosaic is in a far, far weaker place than it was five months ago.”

Earlier in his evidence Lobban admitted that GCHQ collects data from members of the public who are not under any suspicion. But he said that this would never be read or reviewed.

Lobban said: “If you think of the internet as an enormous hayfield, what we are trying to do is collect hay from those parts of the field we can get access to and which might be lucrative in terms of containing the needles or the fragments of the needles that might help our mission.

“When we gather that haystack – and remember it is not a haystack from the home field, it is a haystack from a tiny proportion of that field – we are very, very well aware that within that haystack there is going to be plenty of hay which is innocent communications from innocent people, not just British, foreign people as well.

“So we design our queries against that data to draw out the needles and we do not intrude upon the surrounding hay. And so we can only look at the content of communications where there are very specific legal thresholds and requirements which have been met.

“That is the reality. We don’t want to delve into innocent emails and phone calls. I feel I have to say this. I don’t employ the type of people who would do. My people are motivated by saving the lives of British forces on the battlefield, they are motivated by fighting terrorists and serious criminals. If they were asked to snoop, I wouldn’t have the workforce. They’d leave the building.”

Lobban also gave a guarantee to the former Labour cabinet minister Hazel Blears that neither GCHQ nor the other agencies had acted outside the law.