The 2025 season will mark just his second in the second-tier MotoGP feeder series for Agius.
The Sydney-born rider won the 2023 Moto2 European Championship before stepping up to the Moto2 World Championship this year.
“I am very happy that the team has the confidence in me to let me show my potential next season,” said Agius.
“A big thank you to Jürgen (Lingg), Stefan (Keckeisen) and Wolfgang (Kuhn) and everyone at Intact GP who believe in me.
“It’s been a very good start to the season for a rookie and I think we can build on that next year. I can’t wait to continue the journey with this team.”
Agius sits 15th in the riders’ championship after 10 races.
The 19-year-old recorded a season-best 10th at the most recent British Grand Prix and leads the rookie standings.
Despite having his best finish to date, the young Australian said there is room for improvement.
“It’s certainly not a bad result today, but I’m a bit disappointed with myself because I didn’t manage the race perfectly in the middle,” said Agius after Sunday’s race.
“I missed out on a better result there today, because the pace was there to be in the top six or seven, or let’s say a few positions further up.
“But we know that we finished in the top 10. That’s not too bad considering that we started a bit further back on the grid than normal.
“That made my life a bit more difficult for me. Nevertheless, I’m happy with the work we’ve done, and I’d like to thank the team for their help this weekend.
“We have been working hard since Friday because Silverstone is not the easiest of tasks for a rookie.
“But with 10th place on a tough weekend, we have scored important points and increased the gap in the rookie standings.
“I’m glad that we can start the second part of the season like this.”