On the second day of public hearings, Foreign Office officials said they believed Saddam Hussein's nuclear programme had been dismantled and they had no evidence he was trying to supply chemical or biological weapons to terrorists.
Sir William Ehrman, who was director of international security at the Foreign Office, said ministers had been repeatedly warned that the intelligence on Iraq's chemical and biological programmes had been "patchy".
Despite the warnings, however, Tony Blair told the Commons Saddam did have chemical and biological weapons when he made the case for war on the eve of the invasion in March 2003.
Subsequently, it was found Saddam did not have any weapons of mass destruction, having failed to rebuild his programmes following the first Gulf War.
Sir William listed a series of briefings to ministers which included major caveats about the strength of the intelligence.
In April 2000 the picture was described as "limited to chemical weapons", in May 2001 the knowledge of WMD and ballistic missile programmes was "patchy", in March 2002 the intelligence was "sporadic and patchy".
In August 2002 a briefing noted that "we know very little" about Iraq's chemical and biological weapons work since late 1998, and in September 2002 the intelligence "remained limited".
Just days before the invasion the Government had even received intelligence that Saddam may be unable to use his chemical weapons.
"We did, I think on March 10, get a report that chemical weapons might have remained disassembled and Saddam hadn't yet ordered their assembly," he said.
"There was also a suggestion that Iraq might lack warheads capable of effective dispersal of agents."
However Sir William said that it had not made any difference to the case for war over Saddam's refusal to give up his WMD and co-operate with United Nations inspectors.
"I don't think it invalidated the point about the programmes he had. It was more about use," he said.
"From the counter-proliferation point of view it just proved that he had been lying and that he had prohibited items."
Tim Dowse, who was head of counter-proliferation at the Foreign Office, said that when he took up the post in 2001 Iraq was not seen as the main concern.
"It wasn't top of the list," he said. "I would say we put Libya and Iran ahead of Iraq."
He said that Iraq's nuclear programme was believed to have been dismantled by UN inspectors in the 1990s while the chemical and biological weapons it was thought to possess were not regarded primarily as battlefield weapons.
He said that despite concerns in the United States, there was no evidence that Saddam was prepared to supply chemical or biological weapons to terrorists.
"There had been nothing that looked like a relationship between the Iraqis and al Qaida," he said.
"In fact, after 9/11 we concluded that Iraq actually stepped further back. They did not want to be associated with al Qaida. They weren't natural allies."
Sir William added: "We never found evidence linking him closely to al Qaida and we didn't believe that he was in any way behind the 9/11 bombings.
"We never found any evidence that chemical or biological material had been passed by the Iraqi regime to terrorists."
Mr Dowse said that he had originally attached little importance to intelligence claiming the Iraq had weapons it could deploy within 45 minutes, which subsequently featured heavily the Government's notorious Iraq dossier.
"Speaking personally, when I saw the 45 minutes report, I did not give it particular significance because it didn't seem out of line with what we generally assessed to be Iraq's intentions and capabilities with regard to chemical weapons," he said.
He said he took the 45-minute claim to refer to a multi-barrelled rocket launcher kept ready for deployment by Iraqi forces in the event of conflict.
"It certainly took on a rather iconic status that I don't think that those of us who saw the initial report really gave - it wasn't surprising," he added.
Sir William said that from summer 2002 - at a time when the political pressure was beginning to build - more intelligence on Iraq had started to come in.
Sir Lawrence Freedman, a member of the inquiry panel, asked: "Did it ever strike you that the extra intelligence coming through in 2002 and might not have been wholly coincidental?"
Sir William replied: "No."
He insisted that the Government had never claimed that Iraq represented an immediate security threat.
"We never assessed it as an immediate threat. We said there was a clear and present threat but we never said there was an immediate threat," he said.
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