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He was accused of "making speculative pro-EU statements" that were "beneath the dignity of the BOE" by Conservative MP and Eurosceptic Jacob Rees-Mogg.
"This is what I think is doing your reputation and the reputation of the Bank of England harm," said Rees-Mogg at a hearing in London on Tuesday.
Mark Carney responded robustly: "I'm not going to let that stand."
Panic over the UK's EU referendum pushed the pound to a seven-year low last month and it's a subject that Bank of England officials are treating with caution because of its potential to move markets and inflame political tensions.
Carney spoke so slowly and carefully at one point in the hearing, he was described as a "bomb disposal expert" by Andrew Tyrie, chairman of the Treasury Select Committee.
If that testy exchange showed anything, it was how difficult it will be for the Bank of England to maintain a veneer of objectivity in the lead up to the referendum.
If it warns about the economic and financial fall out of a Brexit, the Bank will be accused of using scare tactics to advocate for Prime Minister David Cameron's campaign to remain in the EU.
When questioned about it, Carney said: "These are my views and my views alone."