A Sydney-based agricultural company says it will fight to save a unique business deal with a Cape York Aboriginal community.

Ecom has been negotiating an agreement with the Napranum community, near Weipa, to develop a large grain and cattle property.

The company says it now cannot go ahead because of Queensland's new tree clearing laws.

Ecom chief executive officer Mark Allen says his company has spent almost three years on the deal.

"We are obviously disappointed with that but it's a reality," he said.

"We're certainly continuing to work with the Napranum people to establish what other options we have but we would like obviously to see this project go ahead in its original form if that's possible."