According to the Mail on Sunday, Ms Chakrabarti made the remark about Mr Begg when she shared a platform with him at a Cage event in 2007.
She told the MoS: 'I have always spoken against antisemitism and all forms of racism. I long campaigned for the release of Mr Begg and all other detainees from Guantanamo Bay. I have never spoken about Israel-Palestine. These three facts are completely consistent and I am disappointed that anyone should attempt to suggest otherwise.'
Ms Chakrabarti was appointed by Labour leader Jeremy Corbyn to head the it inquiry after a series of party members were suspended over allegations of anti-Semitism, culminating last month with Ken Livingstone, a close adviser to Mr Corbyn, who claimed Hitler had backed Zionism.
But the independence of the inquiry was called into question this week, after Ms Chakrabarti, the former head of human rights campaign group Liberty, revealed she joined the party on the day she had been appointed by Mr Corbyn.
