It will initially have 40 dedicated staff operating under first assistant ombudsman Sarah Bendall, increasing to 60 from July.
One in 20 university students are victims of sexual assault and one in six of sexual harassment, according to one study.
Half of the students who complained to their university believed the institution didn't listen or said they didn't get the outcome they needed.
Assistant student ombudsman Sarah Bendall will lead a team of 40 staff. (Diego Fedele/AAP PHOTOS)
Ms Bendall said her team was ready to hit the ground running and had modelled the service to handle about 15,000 complaints a year.
There were concerns about how complaints were handled, including about sexual assault, racism and timing and transparency.
"In general terms, what I'm hearing is what we all know about the need to improve how complaints about sexual violence are handled," she told AAP.
"We're clearly hearing concerns about racial violence, racial vilification, including anti-Semitism and Islamophobia on campus and virtually."
There's optimism about the impact the office will have with studies highlighting barriers to students making complaints, Commonwealth ombudsman Iain Anderson said.
How gender-based violence had been handled was one of the major reasons the office had been stood up, he said.
One in 20 university students are victims of sexual assault, according to one study. (James Ross/AAP PHOTOS)
"There's certainly a strong concern that complaints about gender-based violence weren't being treated appropriately by higher education providers," he told AAP.
"More recently we've seen a lot of concern about anti-Semitism on campus and about people, students, feeling very unsafe and unwelcome on campuses."
The national ombudsman will act independently to investigate complaints and gain insight into the sector to recommend systemic changes.
It won't deal with academic marks or employment issues.
It has been welcomed by the sector's peak body Universities Australia, with CEO Luke Sheehy saying students deserved to be fully supported.
Universities and previous governments had failed students for too long, Education Minister Jason Clare said.
"I hope it's a game changer and it means that students are finally being listened to when the worst happens to them," Mr Clare told AAP.
Education Minister Jason Clare hopes the office will be a "game-changer" for students. (Mick Tsikas/AAP PHOTOS)
Mr Clare will introduce legislation in parliament in the coming days that would give the minister the power to implement a code of conduct requiring action from higher education providers on gender-based violence.
He will table a draft code alongside the bill, forcing universities to comply with the ombudsman's recommendations.
Vice-chancellors will be accountable under the code and universities will have to report to their governing body every six months about progress on prevention strategies and measures they've put in place to address gender-based violence.
Universities will be barred from forcing students to sign non-disclosure agreements and will need to ensure staff are adequately trained or appropriate experts are brought in to support victim-survivors.
Independent-run student accommodation on campuses will be captured by the code if they want to maintain their affiliation with a university.
"Some of the worst instances of sexual assault and sexual violence perpetrated against students happen in student accommodation," Mr Clare said.
"They need to be subjected to this code and the code needs to be enforced in those colleges just like it is in every other part of the university."
1800 RESPECT (1800 737 732)
National Sexual Abuse and Redress Support Service 1800 211 028
Lifeline 13 11 14
Fullstop Australia 1800 385 578
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