Farmers will be hit with “modest” fees under a new national $1 billion biosecurity system, which the federal government describes as the first model to consistently protect the industry from threats of disease and pests.

Agriculture Minister Murray Watt said the plan provided more predictable and long-term funding for biosecurity, which underpins the future of regional and rural communities.

“This budget backs our booming $90 billion agriculture sector through investments that will safeguard its premium status,” Senator Watt said as the budget was handed down on Tuesday night.

The National Farmers Federation had feared producers would be hit with new fees, describing it as a “kick in the guts” for an industry that already paid its fair share.

Budget papers show taxpayers will take on the majority of the cost from July 1, while travellers will pay an increased passenger movement charge and higher fees for importation will contribute up to $350 million next year.

Producers across agriculture, fisheries and forestry will pay a new biosecurity protection levy to create a new “equitable, transparent and accountable” security system.

The budget papers said the biosecurity system would minimise disruption and loss from outbreaks, support better yields through lowered crop damage, maintain access to export markets and simplify clearance of imported goods.

As well, the government has set aside $148.5 million over four years to improve the sustainability of the Murray-Darling Basin, with a statutory review to set out priorities for water management over the next decade as communities and the environment adapt to climate change.

Funded under the environment and water portfolio, $32.7 million will go to reforming the basin’s water markets, including a digital platform to provide minute-by-minute updates and improve transparency.

The National Water Grid will be boosted by $197 million over six years to build three infrastructure projects intended to provide access to safe and reliable water for regional and remote communities.

The budget delivered a total of $1.5 billion in new spending on agriculture, including more than $40 million to continue the Indigenous Ranger Biosecurity Program in northern Australia.

The government will also develop a renewed animal welfare strategy, including the appointment of an independent inspector-general.

By Stephanie Gardiner in Canberra