Monash University Malaysia said its email warning students of disciplinary action if found attending "illegal gatherings" was only a reminder to adhere to laws.
It also apologised for the "wording" of the email, which comes days before the Bersih 5 rally this Saturday.
"Monash University provides an unreserved apology for the wording of the recently issued communication to Monash University Malaysia students regarding illegal gatherings.
"The communication did not properly convey the intent of the message.
"The intent of the message was to remind students that taking part in unlawful assembly is contrary to the laws of Malaysia, and students need to be aware of the consequences of undertaking unlawful activities," it said in a statement.
Malaysiakini yesterday reported that Monash University Malaysia registrar Susheela Nair in an email to students said those found participating or arrested at an "illegal gathering" may face disciplinary action from the university.
Nair did not name the gathering, but made reference to "recent" events.
A Malaysian branch another Australian university, Curtin University Sarawak also issued a similar missive to its students and staff members.
In its later statement, Monash also urged students to "carefully consider their participation in such events". It added that it encourages respect of local laws as it "cares for the wellbeing of all of (its) students".
On Tuesday, Universiti Kebangsaan Malaysia suspended student activist Asheeq Ali for his involvement in the anti-Prime Minister Najib Abdul Razak 'Tangkap MO1' rally in Kuala Lumpur last August.
The Peaceful Assembly Act does away with the need for police permits, but requires organisers to notify authorities 10 days ahead and obtain permission from venue owners.
The right to peaceful assembly is protected under Article 10 of the Federal Constitution.
However, the National Human Rights Commission (Suhakam) said those holding counter-rallies to intimidate others from peacefully gathering are not protected under Article 10.
This comes after the anti-Bersih red-shirts group said it will hold counter-rallies to confront Bersih on the same day.
Bersih plans to hold its demonstration this Saturday in Kuala Lumpur, Kuching and Kota Kinabalu.
It is demanding clean elections, clean government, the right to dissent, strengthening of Parliament and empowerment of Sabah and Sarawak.- Mkini