Prime Minister Theresa May said she was not aware of the claims about Mr Green until last month.
Kate Maltby, who claims Damian Green made inappropriate advances to her, says she told a senior Downing Street aide about his behaviour in 2016.
During her overseas trip, Mrs May told reporters she was "very sad" about having to sack Mr Green.
"I first learnt of these allegations when Kate Maltby wrote about them in the Times", May said in a television interview while visiting a British air base in Cyprus on Friday.
May has sacked her deputy Damian Green due to his misconduct over allegations about pornography on his office computer, leaving the position vacant.
"I recognise that Kate Maltby was obviously extremely distressed by what has happened".
Theresa May is nearly "billy no mates" and most who could replace Damian Green are a threat to her, according to a political commentator.
"He has apologised and I think that's absolutely the right thing to do".
He has denied "hurtful" claims that he downloaded and viewed the X-rated material.
Mr Green reportedly replied: "they never do so let's fix a date soon", to which Ms Maltby is said to have replied: "Great".
Image Text messages between Kate Maltby and Damian Green
She now alleges that she told a Downing Street aide about her claims against Mr Green in September 2016, and she was informed it was part of a pattern of behaviour, and that "the Prime Minister knows".
She has said it is important that people working in Parliament feel they can bring forward any concerns they have to be "treated seriously".
Ms Maltby said she had never called for Mr Green's sacking, but wrote her article because she wanted to change the culture of Downing Street.
When Mr Green left office on Wednesday he said he did not recognise Ms Maltby's version of events, stating: "I deeply regret the distress caused to Kate Maltby following her article about me and the reaction to it".
Her accusations triggered a Whitehall investigation into Mr Green's conduct, which eventually led to him being sacked from the Cabinet for making "misleading statements" about pornography found on his Commons computer.
"In his case I was aware that he was the Deputy Prime Minister and I was aware that No 10 knew about it".
Metropolitan Police Commissioner Cressida Dick said Scotland Yard had referred the two retired officers to the Information Commissioner's Office over possible breaches of data protection legislation.
Mr Johnson has also warned Russian Federation of Britain's offensive cyber capability, the Daily Mail reports, as the Foreign Secretary arrived in Moscow for talks with his counterpart Sergei Lavrov.
Health Secretary Jeremy Hunt said the behaviour of the former officers did not "sit comfortably in a democracy".
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