Roddy Dunlop QC said he and his colleagues disagree with statements that were contained on a video made by the government department.
The recording, which was posted on social media, states that the current asylum system was “open to abuse”, allowing lawyers to “delay and disrupt returns” of people.
However, Mr Dunlop said: “Faculty shares the condemnation of attacks on lawyers as ‘activists’ in the Home Office video.
“Lawyers pleading their clients’ case in accordance with the law are not ‘activists’. They are lawyers. Any lawyer pulling his or her punches because the Home Office (or anyone else) doesn’t like it isn’t doing the job properly.
“Independence of thought and fearless scrutiny of executive power is essential to the rule of law, and should not be denigrated by any government.”
The animated clip was recently published on the government department’s Twitter feed and referred to crossings of the English Channel by asylum seekers in small boats.
It showed a graphic of planes leaving the UK, with the caption: “We are working to remove migrants with no right to remain in the UK.
“But currently return regulations are rigid and open to abuse... allowing activist lawyers to delay and disrupt returns.”
The Law Society, which represents English and Welsh lawyers, also condemned the video saying it undermined the rule of law.
Home Office permanent secretary Matthew Rycroft said the video “should not have been used on an official government channel” and would not be posted again.
Mr Dunlop recently took over as Dean from Gordon Jackson QC, the senior lawyer who represented former first minister Alex Salmond’s during his recent acquittal on sexual assault charges.
Mr Dunlop is currently acting for David Whitehouse, the former Rangers administrator who is suing prosecutors and the police for £10.5 million for wrongful arrest.
Mr Whitehouse secured a £350,000 payment for his £1.8m legal bill on Wednesday after the Lord Advocate’s lawyers admitted the prosecution against him was “malicious”.