Lord Turnbull was the UK's top civil servant during the war
Ex-No 10 spokesman Alastair Campbell has been attacked for suggesting Clare Short was barred from key Iraq meetings because she could not be trusted.
Former head of the Civil Service, Lord Turnbull, said his remarks were "very poor" and Ms Short's critical stance on the war should have been respected.
He said Tony Blair must explain claims that he would have backed the war even if he had known Iraq had no WMD.
Mr Blair is due to give evidence to the inquiry in the next few weeks.
Lord Turnbull is the latest senior figure to give evidence to the Chilcot inquiry, which is looking into the controversial invasion in March 2003 and the aftermath of the war.
As Cabinet Secretary from September 2002, he was in Downing Street playing a key role in the run-up to the war and afterwards.
He defended the conduct of Clare Short, the International Development Secretary, who resigned from the cabinet two months after the war in protest at post-war planning.
Ms Short has been criticised by several senior military figures while Mr Campbell said she was "difficult to handle" and suggested that she was barred from key meetings amid fears sensitive information would leak.
Lord Turnbull said such criticism of Ms Short was "patronising".
While she could be "troublesome and strong-minded", he believed Ms Short had been marginalised as she had a "distinct view" on Iraq which did not conform with No 10 policy.
"Tony Blair wanted things to move quickly," he said. "He did not want to spend time on 'conflict resolution' between colleagues."
Lord Turnbull spoke of a policy "consensus" from September 2002 onwards - at which point he said the UK was seeking to disarm Saddam Hussein through the UN but was also planning for military action.
Alternative options were ignored, he suggested, while civil servants found it hard to challenge the prevailing view.
AT THE INQUIRY
BBC World Affairs correspondent Peter Biles
The inner workings of government might be considered "boring", to quote Sir John Chilcot today. But the Inquiry is showing how important they can be.
Clare Short's concern over her exclusion from key meetings in 2003 has been highlighted by the release of declassified government letters.
On 11 March, the permanent secretary at the Department for International Development (DFID), Sir Suma Chakrabarti, wrote to the cabinet secretary, Lord Turnbull, about the government's communication strategy on Iraq. "More frequent and systematic discussion between senior ministers would be helpful
in addition, Clare Short and the prime minister need to talk more often, probably on a daily basis".
Earlier today, we heard evidence from the first female witness to appear before the Inquiry. Dr Nemat Shafik, who succeeded Sir Suma at DFID in 2005, said the main lesson from Iraq was the need for honesty from political leaders when assessing the timescale for development and reconstruction.
Throughout the period leading up to war, Tony Blair had been "unambiguous" that disarming Saddam was his primary objective.
So he questioned a recent BBC interview in which Tony Blair said he would still have supported ousting Saddam Hussein even if he had known beforehand that Iraq had no weapons of mass destruction.
"The question is what on earth is this statement to Fern Brittan on the television all about? You will have to put this point to him."
And, on reflection, he felt Mr Blair had used language backing regime change ever since meeting President Bush in the US April 2002 and had had to adjust his thinking to win support.
"My hypothesis is he starts as a regime changer," he said.
"Then, it is not just Bush who is put onto the UN route but Blair also. At that point he is either saying I am really a "regime changer" but I will talk the disarmament language or he realises that disarmament...is the only way he thinks of toppling this regime."
Lord Turnbull told the inquiry how decisions were made by a group of key advisers and ministers in the run-up to the war, which he described as "serious players" meeting in an "informal environment".
Asked about cabinet discussions on Iraq in the immediate run-up to war, he said there were serious debates in which most members spoke but key decisions were taken elsewhere.
He suggested the cabinet never discussed the advice given by Attorney General Lord Goldsmith on the legality of the war.
Cabinet members were supportive of government policy and the late Robin Cook was the only minister willing to argue in cabinet that containment of Saddam Hussein was working.
"I am sorry he's not around to take the credit for that," he said.
The failure of UN weapons inspectors to find a "smoking gun" in the run-up to the conflict made Cabinet ministers more convinced Saddam was concealing weapons and not co-operating, he added.
Lord Turnbull identified April 2004 as the point in which the coalition realised things were going badly wrong in Iraq.
He said he had felt "sullied" about the disclosure of prisoner abuse by US soldiers at Abu Ghraib prison.
"It was a very distasteful revelation and shocked a lot of people. It made it apparent what an uneasy partnership this was."
He suggested cabinet support for the policy could have "fractured" at this point but ministers showed strong loyalty to Tony Blair.
Despite his misgivings about the policy process, Lord Turnbull said he still believed it had been "worthwhile" to remove Saddam Hussein.
It was clear that Saddam had lied about his intentions in order not to demonstrate weakness to Iran and he planned to rebuild his chemical and biological weapons capacity once sanctions were lifted.
The British people must be apprised of this to counter the prevailing view that the deaths of UK soldiers had been "in vain".