Christophe Arend, an MP in the La Republique En Marche (LREM) party, "disputes the facts" and has countered with a slander claim, his lawyer said in a statement.
The 29-year-old woman, identified under the pseudonym Marie, told Franceinfo that her ex-boss had "tried everything to get me to give in" with repeated "sexist comments" and inappropriate gestures.
"For example, he tries to unstrap my bra when walking by, to touch my breasts," she said.
Marie led Arend's campaign during this year's legislative elections, when he made headlines in June by beating out Florian Philippot, then the vice president of the far-right National Front.
She was then hired as his parliamentary assistant. "I was hoping that our relation would become more professional once I had an employment contract. I thought I would be more protected," she said.
But she quit in late July.
Macron's parliamentary group said it "took note of the serious accusations against Christophe Arend",
"All forms of violence and harassment are inacceptable," it said in a statement, adding that it was up to the courts to investigate the claims.
A growing number of French women have been revealing stories of harassment and abuse at the hands of men in the wake of the accusations against Hollywood mogul Harvey Weinstein.
The #Balancetonporc (Expose your pig) hashtag, based on the #MeToo campaign, has touched a nerve in a country that has long been seen as too soft on sexual harassment.
- Women in Paris tell their stories of being groped, pestered and sexually harassed
- 'Squeal on the pigs': French women bombard Twitter with tales of sexual harassment
- Men in France to face on the spot fines for sexually harassing women
This week, the writer Ariane Fornia, daughter of a minister in the government of former president Nicolas Sarkozy, accused a top Socialist leader and advisor to ex=president Francois Mitterrand of assault while attending the Opera Bastille in Paris in 2010.
Pierre Joxe, 82, a former member of France's Constitutional Council, rejected the claims, telling AFP: "I will address this subject at length in writing next week, after taking the time to analyse the details of this matter."
Fornia's father, Eric Besson, told French magazine L'Express he was "enraged" after learning about the incident.
"I thought about going and waiting for Joxe to leave his home, so I could beat him up," he said.
"Then I listened to my daughter's worries, at what was a delicate time for me politically and which was affecting her as well. We kept quiet."
And on Friday, Gilbert Cuzou, a member of the greater Paris regional council, said he would cooperate with police after two female associates accused him of assault and harassment.
His political group, the Ecological and Social Alternative, said it had excluded Cuzou during the investigation.
"After discussing with my lawyer, I will file a libel suit after these accusations," the 34-year-old Cuzou said.