Lord Justice Leveson has ordered an investigation into security procedures at his inquiry into the media after a protester burst into the courtroom to shout at Tony Blair while the former prime minister gave evidence.

The man, wearing a white shirt and chino trousers, entered from behind a curtain almost directly behind Leveson himself, inside court 73 at the Royal Courts of Justice.

The protester, later named as David Lawley-Wakelin, 49, shouted: "Excuse me. This man should be arrested for war crimes. JP Morgan paid him off for the Iraq war; three months after we invaded Iraq they held up the Iraq bank for £20bn. He was then paid $6m every year, and still is, from JP Morgan, six months after he left office. The man is a war criminal."

Several security guards tackled the man and dragged him away through the same door through which he had entered.

Leveson, appearing shocked, stood up from his seat to watch as the protester was ejected. He asked the court how the man had gained entry. "I'm sorry for that, Mr Blair," Leveson said.

"I'd like to find out how this gentleman managed to access the court through what is supposed to be a secure corridor, and I'll have an investigation undertaken about that immediately." He ended: "I apologise."

Blair, who sat impassively throughout the intrusion, sounded slightly shaken as he answered: "That's fine." He continued: "Can I just say, actually, on the record: what he said about Iraq and JP Morgan is completely and totally untrue. I've never had a discussion with them about that [Iraq]."

Leveson told the former prime minister that he did not need to respond to the intruder's accusations.

Blair replied: "I appreciate that, but part of the difficulty with modern politics – and this is not a criticism of the media – is that my experience of the reporting of these events is that you can have 1,000 people in a room and someone gets up and shouts or throws something, and that's the news. The other 999 might as well not have bothered turning up."

As the protester was bundled away he told reporters he was a freelance documentary film-maker who has made a 45-minute film entitled The Alternative Iraq Enquiry.

Lawley-Wakelin has been in the spotlight before: on the BBC's Question Time programme he once accused Blair of being a liar prepared to kill for oil.

On Monday he breached a secure area for court staff and jumped into the courtroom. The judge's bench is accessible only to Leveson and his court staff, using a swipe card.

One uniformed police officer, who had accompanied Blair in the witness seating area, bounded past Robert Jay, lead counsel to the inquiry, to bundle Lawley-Wakelin out of the court. Two other plainclothes police officers who were part of Blair's party quickly followed suit.

The court service also had its own two security staff – one stationed inside court 73 and one outside, sitting at the entrance used by the press and public.

The protester was taken by about half a dozen security men to the east block of the high court and held in a secure zone, where he was detained until police arrived and arrested him.

"He has been arrested on suspicion of breach of the peace," said a spokesman for Scotland Yard. "He is currently in custody at a central London police station."

Leveson resumed the inquiry at 2pm, apologising once again to Blair and promising that "efforts will be redoubled" to ensure there would not be a repeat of the morning's drama.

In an opening statement he said: "The inquiry and Her Majesty's Courts and Tribunals Service, which is responsible for security in this building, take the incident this morning extremely seriously. Considerable effort has been put into ensuring all witnesses can give their evidence in a safe and secure environment and I very much regret what has happened and I will be giving consideration to the steps that can be taken and should be taken against this particular intruder.

"Efforts will be redoubled to ensure that incidents of this nature do not recur.

"I repeat my apology to Mr Blair and indeed to everyone else who was involved in or following the inquiry," said Leveson.

The investigation is being led by David Thompson, the director of the Royal Courts of Justice.

Since leaving office in 2007 Blair has been regularly targeted by protesters over his central role in pushing for the US-led invasion of Iraq in 2003. In January last year he was greeted by dozens of activists outside the Queen Elizabeth II conference centre in central London as he returned to give evidence to the Chilcot inquiry into the genesis of the conflict.

• This article was amended on 29 May 2012 to clarify remarks made by the protester.