The intruder, who told reporters his name was David Lawley Wakelin, managed to evade security and access the room through a back corridor.
The 49-year-old, who made a film called The Alternative Iraq Enquiry, brought proceedings to a halt by hurling accusations at the former Prime Minister.
He said: “JP Morgan paid him off for the Iraq war. Three months after he invaded Iraq they held up the Iraq bank for $20 billion.
“He was then paid $6 million every year and still is from JP Morgan six months after he left office. This man is a war criminal.”
He was eventually wrestled to the ground by three men, ejected from the courtroom and arrested.
Lord Justice Leveson, who rose to his feet when the intruder entered, called for an inquiry into how he had got in.
“I would like to find out how this gentleman managed to access the court through what’s supposed to be a secure corridor, and I’ll have an investigation undertaken about that immediately,” he said.
After the removal of the protester, Mr Blair denied his allegations.
He told the hearing: “What he said about Iraq and JP Morgan is completely untrue. I’ve never had a discussion with them about that.”
After leaving office, Mr Blair advised the investment bank in return for a reputedly giant pay packet.
The protester was escorted through the Royal Courts of Justice by security guards and was seen being driven away in a police van.
It is understood he got past security-coded doors to access the judges’ corridor leading to courtroom 73.
Scotland Yard said he Mr Lawley Wakelin had been arrested on suspicion of breach of the peace and was held in custody at a central London police station. He was released without charge.
Mr Lawley Wakelin said later it had been “surprisingly easy” to get into the inquiry.