Six people have been arrested in Melbourne's CBD after a clash between pro-Palestinian and pro-Israeli rallies on Sunday.

Police said approximately 7,000 people were in attendance across the two separate rallies.

"While the organisers had confirmed separate locations and routes for their events, protesters from one group moved to … counter protest," police said in a statement.

"To ensure safety and prevent violence, Victoria Police were required to form lines between the two opposing groups.

"The police response was largely successful in keeping these two opposing groups separate."

The six people who were arrested were released and will receive a summons to appear in court, police said.

During the rallies, one person was seen burning an Israeli flag.

Liberal Senator and Shadow Minister for Home Affairs James Patterson was among several political figures attending the pro-Israeli demonstration.

"I think it's really important as Australians that we stand up and say that the anti-Semitism that we've seen in our country, particularly in the last six months, is completely unacceptable," Mr Patterson said.

"This is not a rally about the Middle East, this is not a rally about conflict, this is a rally about Australia and who we are as a country and we should never tolerate the hate that we've seen in our community."

Sunday's events come after a week of protest activity throughout Melbourne.

On Saturday, pro-Palestinian demonstrators stormed a Labor Party conference in the city's north-west where Prime Minister Anthony Albanese was in attendance.

During the week, university protests were in the spotlight.

Pro-Palestinian encampments have been established at a number of campuses across Australia.

In Melbourne, students were this week occupying a building in the CBD belonging to the University of Melbourne.