Mr Duncan Smith, who campaigned for Leave alongside the now Foreign Secretary, bashed pro-EU politicians for their immature behaviour over Brexit.
Speaking to Sky News the MP for Chingford and Woodford Green said: “You can always take stuff out of context.
“I know Boris very well, I talk to him endlessly I fought the campaign with him I know what his private and his public views are.
“What he has always said is he is not against migration but he is in favour of controlled migration.
“We don’t have control in the EU only by leaving do we actually get that.”
He continued: “It is easy to say he likes the idea of freedom of movement but what he is actually saying is it has to have constraints.
“And that is what you mean by controlled migration. All over the European capitals a number of politicians are behaving like children.
“The puerility of people behaving like children in various capitals around Europe, threatening everything – all that will fade away.
“The real business of the grown ups is to get on and sort this out so that we have a proper arrangement.”
Mr Duncan Smith, a lifelong eurosceptic, said a free trade agreement between Britain and the EU would benefit both sides.
Mr Johnson ignited a political fire after it was reported he had told multiple EU diplomats that freedom of movement across the EU “corresponded” to his own beliefs.
One told Sky News: “Boris Johnson told us he was personally in favour of it, but he said that Britain had been more affected by freedom movement of people than other EU member states.
Another added: “He did say he was personally in favour of free movement, as it corresponds to his own beliefs. But he said it wasn’t Government policy.”
Mr Johnson’s team has angrily denied the reports, with one source telling The Telegraph they were a “total lie”.
A spokesman said: “Boris said what he has said many times before – he is pro-immigration but wants to take back control to limit numbers.
“He did not say he supported freedom of movement and challenges anyone to show proof that he ever said that.”
Shadow Brexit secretary Keir Starmer said: “We are seeing a situation now almost on a daily basis where there are leaked memos, there are photographed documents.
“And we have Boris Johnson with almost a running commentary. Whether it is to Czech newspapers or to ambassadors.
“It is becoming a complete mess. I think the Government needs to correct this now.”