Last week Airbus said a no-deal Brexit would threaten their future in the UK.
Jeremy Hunt slammed the comments as “completely inappropriate”.
According to the Wetherpoons chief, Airbus has been dishing out pro-EU statements for “a long time”.
Speaking on BBC Newsnight, he said: “I think it’s a fair point for Airbus to make.
“They’ve been saying this sort of thing for a long time.
“They were very much in favour of us entering the Euro and they were very vociferous about that.
“They were very vociferous and even wrote to their own employees to say that they should vote in favour of Remain in the referendum.
“They’re very pro the EU. They like the EU.”
However, Mr Martin elaborated and said these sorts of comments would have been more appropriate in a debate and the Government is right to hit back.
Mr Martin said: “Should they be allowed to speak?
“Yeah, well probably they should as long as it can be debated on a programme like Newsnight, I think it’s right.
“But is the Government right to tell them to shut up? Yes!”
Tim Martin has been a vocal supporter of Brexit and last week claimed that leaving the bloc could “immediately” save the UK £10billion each year.
Speaking on BBC Question Time last week, the panel was debating how to give the NHS extra funding after Brexit if the UK did not receive the dividend promised by Theresa May when we leave.
The founder of the popular food chain did not entertain the negative scenario and triumphantly announced: “We immediately save £10billion a year when we leave the European Union.”
The Brexit dividend is the annual contribution the UK pays towards the bloc’s budget every year.
Once the UK stops paying into the EU budget, the Office for Budget Responsibility (OBR) says there will be savings.
The arch-Brexiteer said: “I think this essence of Brexit is that there will be a dividend and the people who voted for it will think there is a dividend.”
Under the Tories current plans, the UK will remain a member of the EU until 29 March 2019 and will pay into the budget until then.