Labor wants laws protecting gay students from being excluded by religious schools extended to teachers and staff.
"In my discussions with religious educators, it's clear this is not an exemption that they use or want to use," Shorten said on Monday.
"These laws are no longer appropriate, if indeed they ever were appropriate. It's time our laws reflected the values we teach our children."
Prime Minister Scott Morrison on Monday told parliament he had written to Shorten about the need to act on discrimination of students by religious schools "over the next fortnight" in order to deal with "the unnecessary anxiety that's been created for children and their parents", but would not comment on the same protections being offered for teachers.
Labor's Tony Burke asked Morrison to table the Philip Ruddock review, which has still not been released, but Speaker Tony Burke said it was referenced, not used, and therefore did not need to be.
Earlier in the day Education Minister Dan Tehan had said protecting LGBTI students from discrimination was a top priority for the coalition as MPs returned to Canberra after a three-week break.
"We want to deal with the issue of students ... I expect that something will be done over the coming days on that," Tehan told Sky News.
However, the minister would not say whether the same legislative support would be extended to gay teachers.
He acknowledged the issue needed to be investigated, but said it was complicated.
Senator Derryn Hinch tried unsuccessfully to move a motion which would mean any schools found to discriminate against LGTBIQ students or teachers would lose their Commonwealth funding.
Former prime minister Tony Abbott said he was mystified by the debate, saying there was no evidence gay kids had been discriminated against by religious schools.
Debate around discrimination against gay students and teachers has flared up in the past week, after the recommendations of a review into religious freedoms were leaked to the media.
The review, led by former attorney-general Philip Ruddock, did not recommend the removal of existing laws allowing faith-based schools to discriminate on the basis of sexuality.
It said the laws should be amended so religious schools publicly outlined their policies and provide them to workers.
However, Prime Minister Scott Morrison has decided to abolish the exemptions to anti-discrimination laws altogether.
Even still, Morrison concedes the prospect has been causing anxiety, and wants the issue dealt with swiftly.
Most voters are against laws which allow religious schools to select students and teachers based on their sexuality.
Three-quarters of respondents to a Fairfax-Ipsos poll rejected the exemptions to discrimination laws, including a majority of coalition, Labor, Greens and One Nation voters.
The Ruddock review was handed to the federal government in May but it is yet to provide a full response.