A handful of protesters chained themselves to temporary fences in Melbourne as others yelled '"Free Palestine" and held signs that read "Stop the genocide".
Around a dozen angry protesters congregated outside the consulate, with some making speeches.
A heavy police cohort cleared out the defiant protesters, with two arrested for obstructing police.
One protester said the group was demanding the closure of Pine Gap, an Austalian-US military base outside of Alice Springs.
"We are here today to demand the closure of Pine Gap.. where the information sourced there is used to continue the colonial occupation of Palestine by the forces of Israel," the protester said.
In Alice Springs, a group of protesters blocked the entrance to the Pine Gap facility just before 5am.
No arrests were made in the Northern Territory.