The prime minister not only knew about the allegations, officials said, but suggested that he might make a return to serve in her government.
The politician, who denies any wrongdoing, initially tried to settle the matter informally with a letter of apology to the woman before reaching a financial settlement in the summer.
A second official has also claimed that the minister, who was part of Boris Johnson's government, made harassing comments to her, which he also denies.
Claims of his links to Ms Truss come at the end of a difficult Tory conference for the prime minister and put further pressure on her refusal to appoint a parliamentary ethics adviser after Mr Johnson scrapped the role earlier this year.
She dismissed calls to do so, saying during her campaign that she knew the "difference between right and wrong".
The Independent understands that the former minister provided some support behind the scenes for the Truss leadership campaign despite her being aware of the allegations, according to two No 10 officials.
She was among a clutch of cabinet members, including Mr Johnson, who were told informally of allegations, sources said. No formal investigation was carried out.
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