The Will Smith sci-fi comedy unseated Sacha Baron Cohen's The Dictator after it had spent just a week at the top of the standings.
Men in Black 3 also topped the US box office standings this weekend.
Robert Pattinson's Bel Ami is the only other new entry in this week's top ten, while Judi Dench and Dev Patel's comedy-drama The Best Exotic Marigold Hotel continues its strong showing in its tenth week on the chart.
The Australian box office top ten for the weekend of May 24 to May 27 in full (All takings shown in Australian dollars):
1. (-) Men in Black 3 - $5,001,861
2. (1) The Dictator - $2,452,796
3. (2) The Avengers - $2,262,900
4. (3) Dark Shadows - $1,136,216
5. (4) The Five-Year Engagement - $465,531
6. (-) Bel Ami - $264,521
7. (6) The Best Exotic Marigold Hotel - $195,228
8. (5) The Woman In Black - $180,199
9. (8) Salmon Fishing in the Yemen - $145,475
10. (9) The Way - $143,084
Watch Men in Black 3 star Josh Brolin talking to Digital Spy below:
Photo gallery - 'Men in Black 3' premiere: