The Government says it is delivering "smarter services" for biosecurity and the primary sector by providing pragmatic solutions.
There was additional capital funding of $6.7 million and operational funding of $14.3m over four years to replace ageing border clearance systems run by the Ministry of Agriculture and Forestry (MAF) and the Customs Service with a single joint border management system (JBMS).
"The JBMS will improve efficiency and biosecurity protection," Mr Carter said.
Its single portal for importers and exporters would collect shared services, hosted predominantly by Customs, for clearance of passengers and goods.
He also noted the budget confirmed $45m over four years for the Global Research Alliance on Agricultural Greenhouse Gases to help nearly 30 countries collaborate on producing more food with fewer emissions.
Mr Carter said the potential gains from equipping farmers with the latest research on their farm greenhouse gas emissions "cannot be underestimated".
But the spending was earlier this week decried by Federated Farmers president Don Nicolson, who said that the money had been promised "in the hope of a eureka moment".
"New Zealand's funding for international collaborative research works out at $11m annually, the United States is chipping in around $26m a year, while Canada is putting in just under $10m," he said.
"So New Zealand's international research contribution into supposedly the 'biggest crisis facing Planet Earth,' is equivalent to one referendum or about a quarter of what's spent each year just to support our 122 MPs."
After today's budget -- which Mr Carter said delivered "real and long-lasting solutions" -- Federated Farmers said it welcomed budget support for sustainable growth, but said there was little direct benefit for vote agriculture and more needed to be done to get the desired growth in the trade sector.
"The $5.25 million in new spending for New Zealand's largest export industry seems small compared to what other ministries won," said spokesman Philip York. The $5.25 million for biosecurity "seems miniscule" because it was protecting $25 billion in annual exports.
The farm lobby had called for spending restraint, but biosecurity needed more money.
Meat industry board Meat and Wool NZ welcomed the Government's injection of cash into science,and the board chairman Mike Petersen said government support enabled the industry's annual $11m investment in research and technology transfer to be leveraged to a significant portfolio of $20m to pastoral sector research.