Downing Street said in a statement that Truss had asked minister for trade policy Conor Burns "to leave the government with immediate effect".
"The prime minister took direct action on being informed of this allegation and is clear that all ministers should maintain the high standards of behaviour -- as the public rightly expects," it added.
Burns, who was a parliamentary private secretary or unpaid assistant to Johnson when he was foreign minister, has also been temporarily suspended from the parliamentary Conservative party.
The whips' office, which is responsible for party discipline, said that followed "allegations of inappropriate behaviour earlier this week".
"We take all such allegations extremely seriously. The prime minister has been clear that the highest standards in public life must be upheld," it added.
British media quoted Burns as saying he would cooperate with the investigation and was looking forward to clearing his name.
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