Hirani has categorically denied the allegations. His lawyer Anand Desai termed the allegations "false, mischievous, scandalous, motivated and defamatory".
In an article on HuffPost India, the woman, who calls herself "an assistant", alleged that Hirani sexually abused her more than once between March and September 2018.
She detailed her allegations in an email dated November 3, 2018, to Hirani's longtime collaborator and "Sanju" co-producer Vidhu Vinod Chopra.
The woman said that on April 9, 2018, the director first passed a sexually suggestive remark to her and later sexually assaulted her at his home office.
"I remember forming these words on my lips - 'Sir, This is wrong. Because of this power structure. You being the absolute power and me being a mere assistant, a nobody - I will never be able to express myself to you'," she wrote of the April 9 incident in the email to Chopra, as quoted by the article.
The woman said that Hirani was a father figure for her.
"My mind, body and heart were grossly violated that night and for the next 6 months," the email read.
Chopra's wife, film critic Anupama, who is a director at Vinod Chopra Films Pvt Ltd, "Sanju" scriptwriter Abhijat Joshi and filmmaker Shelly Chopra, Vidhu Vinod's sister, were also marked on the email.
The complainant later said to HuffPost India that she was "intimidated by Hirani", who was her reporting person at the time.
She said she maintained a facade of normalcy regarding Hirani's behaviour as she needed to hold on to her job as her father was suffering from a terminal illness.
"I had no choice but to be polite to him. It was unbearable but the reason I endured it all, until I couldn't, was because I didn't want my job to be taken away from me, and work to be questioned. Ever."
"I was worried that if I left midway, it would be impossible to find another job in this industry if he were to speak badly about my work. Because if Hirani said I wasn't good, everybody would listen. My future would be in jeopardy," she said.
Anupama Chopra had confirmed that the woman had shared an account with her and that Vinod Chopra Films (VCF) has since set up a committee to address complaints of sexual harassment.
"I have offered my full support and recommended that she take the complaint to a legal body or a neutral party since we cannot be arbitrators or judges on this. "We also offered to set up an ICC at VCF (which we have set up since then) even though a VCF ICC could not have taken up the case since she was an RHF (Rajkumar Hirani Films) employee at the time. These are two separate companies," she said in an email dated December 5, 2018.
Anupama said the woman told her she needed time to think about how to take things forward.
She added, "I did not want in any way to pressurise her or steer her in any direction. As Vinod and I told her then, she has our full support and we are fully respectful of whatever decision she has taken."
The development comes close on the heels of Hirani's name been dropped from the new poster and trailer of "Ek Ladki Ko Dekha Toh Aisa Laga", directed by Shelly Chopra.
A still from the film's teaser, which released on 27 June, 2018, carried Hirani's name as co-producer. Vidhu Vinod Chopra has not yet commented.
Hirani's is the latest name to be called out in India's #MeToo storm, which has engulfed many a stalwart such as Nana Patekar, Alok Nath, Vikas Bahl, Sajid Khan and former Union minister MJ Akbar, among others.
The woman making the allegation worked with Hirani on his 2017 film Sanju.'I had no choice but to be polite to him. It was unbearable but the reason I endured it all, until I couldn't, was because I didn't want my job to be taken away from me, and work to be questioned. Ever,' she said.