Tony Fleming, the department’s director, said the pact would give the Githabul a "much greater involvement" in the management of the land.
"I think for a lot of our visitors to national parks, it adds a huge dimension to their experience," he told ABC radio.
"They’ll get access to the knowledge of the Githabul people, the interpretation of this part of the state from an Aboriginal perspective, and we as land managers learn a lot from Aboriginal people about how to look after these sorts of places."
Aborigines, many of whom live in poverty, have been battling to reclaim their traditional lands, and in the early 1990s, Australia's highest court cleared the way for such native title claims.
In September, a federal court ruled that the Noongar people were the traditional owners of a 6,000sq km area of Western Australia state that includes its capital, Perth.
The court ruled that the Noongar had, against the odds, maintained their culture and customs since the European settlement in 1829 and had native title over the land.
But the federal government has appealed against the decision, saying that it could restrict people's access to parks and other public land.