The agreement only applies for telephone and walk-in bookings however and not those marketed or published online, Reuters reports.
The deal, following an investigation, comes after Germany’s antitrust regulator ordered Booking.com to stop forbidding hotels to offer rooms at lower prices on their own websites.
Similar changes have been made in Italy, France and Sweden, Reuters reports.
"They will now be able to offer lower rates through telephone bookings and walk-ins, offer special rates and deals to customer loyalty groups,
in addition to offering deals via Expedia and Booking.com," Australian Competition and Consumer Commission chairman Rod Sims said in a statement.
Global hotel chains like Hilton Worldwide Holdings and Accor SA have focused on expanding their loyalty programmes and offering discounts and perks to members to encourage customers to make direct bookings.