Dominic Raab ignored repeated warnings about his behavior, said a retired senior official who worked with him at the Foreign Office.
Lord MacDonald described his former boss as a “disciplined” whose methods failed to help him achieve his goals.
He told the BBC that he had raised the issue with Mr Raab more than once, but he had “denied it” and was unwilling to listen.
The former deputy prime minister resigned on Friday following a bullying investigation and apologized if he upset anyone.
An investigation found he was “intimidating” and “aggressive” towards police, but Mr Raab said his behavior was not bullying and almost all complaints against him were dismissed.
It dealt with eight formal complaints about Mr Raab’s conduct as justice secretary, foreign secretary and Brexit secretary.
Lead counsel Adam Tolley KC, who led the investigation, concluded Mr Raab’s conduct involved “abuse or abuse of power” and that he had treated police in an “intimidating manner” and “continuously aggressive”.
Mr Tolley said he found Mr Raab describing bullying when he was foreign secretary and justice secretary.
But referring to complaints made during his tenure as attorney general, Mr Tolley concluded that Mr Raab had “no intention of angering or humiliating himself by the conduct he described” and had not “targeted anyone with any particular type of treatment”.
In an exclusive interview with BBC Radio 4’s Today programme, Lord Macdonald, who is Mr Raab’s foreign office permanent secretary, said: “I’ve seen a tough watchdog. I’ve seen a minister who knows what he wants to do.
“Honestly, I’ve seen some guys and his approach didn’t help him achieve what he wanted to do, and I’ve spoken to him about it more than once.”
Asked if Mr Raab wanted to hear it, he replied: “No, he denies it, he denies that description.”
Lord MacDonald said he did not use the word “bullying” against Mr Raab partly because things were not ready at the time.
“I’ve been trying to get my boss to understand how his behavior is making his career difficult. I’m trying to help him get the best out of his team, and I think calling bullying is too aggressive,” he said.
Lord Macdonald was not at the Foreign Office at the time of the investigation’s reports and confirmed incidents.