Brittany Higgins said she had feared losing her job after the 2019 incident, and had little support from her bosses.
Ms Higgins, 26, gave a TV interview on Monday that has prompted shock and outrage over her treatment.
Mr Morrison apologised for the way Ms Higgins' complaint was handled.
The allegations are now under a renewed police investigation.
Mr Morrison said he was "shattered" by her claims, and had called for a review into parliament's environment and culture.
"I hope Brittany's call is a wake-up call for all of us," he told reporters in Canberra on Tuesday.
But Mr Morrison was also drew criticism for saying he better comprehended the allegations after considering them as a father of two girls.
She said she was offered her a lift home by an older male colleague at the end of a night out, but instead he took her to Parliament House.
Ms Higgins said she was drunk and feel asleep in Defence Industry Minister Linda Reynolds' office, before waking to find the man sexually assaulting her.
"I woke up mid-rape essentially," she told Network Ten. "I started crying... I told him to stop."
She said the man left immediately afterwards, and she wasn't offered assistance by security guards on her way out of parliament.
In the days following, Ms Higgins said she felt Ms Reynolds' office aimed to "manage" the situation, downplaying her trauma.
"It felt like I became... it immediately became a political problem," she said.
Ms Higgins said Ms Reynolds told her she would be supported if she pursued a police complaint, but she ultimately chose not to in 2019 because she believed it would jeopardise her career.