The former prime minister's wife, who sits as a judge as Cherie Booth QC, told Shamso Miah that she would suspend his prison sentence because he was a "religious man".
Miah, a devout Muslim, had been convicted of breaking a man's jaw with two punches after a dispute in a bank queue in East Ham, London. The 25-year-old had gone to the bank from a local mosque.
Miss Booth, who has made no secret of her strong Roman Catholic faith, appeared to indicate that she was taking into account Miah's religious beliefs as she opted for a lenient sentence.
“I am going to suspend this sentence for the period of two years based on the fact you are a religious person and have not been in trouble before," she told him at Inner London Crown Court.
"You caused a mild fracture to the jaw of a member of the public standing in a queue at Lloyds Bank. You are a religious man and you know this is not acceptable behaviour.”
The National Secular Society has lodged an official protest with the Office for Judicial Complaints (OJC), claiming that Miss Booth was effectively discriminating against atheists.
Terry Sanderson, president of the NSS, told The Daily Telegraph's Mandrake column: “This seems to indicate that she would not have treated a non-religious person with the same latitude. We think this is discriminatory and unjust.”
The OJC was established in 2006 to handle complaints against members of the judiciary. If the protest is deemed worthy of investigation the OJC can demand that Miss Booth gives a written account of her decision.
It is also able to appoint senior judge to carry out a full inquiry, which could result in formal disciplinary action.
