"I consider these four arrangements to be inconsistent with Australia’s foreign policy or adverse to our foreign relations," Senator Payne said.
It is the first time the federal government has used the new veto powers, which permits it to cancel agreements states and territories strike with other countries.
The Belt and Road deals tied Victoria to Chinese President Xi Jinping's major infrastructure project.
Agreed areas of cooperation included increasing participation of Chinese infrastructure companies in Victoria's infrastructure construction program and promoting cooperation of Victorian businesses in China.
Victorian Premier Daniel Andrews late last year said scrapping the agreements would be risky and they could bring jobs and investment to the state during its coronavirus recovery.
China has in the past 12 months launched a series of damaging trade strikes against Australia after Prime Minister Scott Morrison called for an independent inquiry into the origins of the pandemic.
The Chinese government also remains furious with Australia over foreign interference and investment laws and the decision to ban Huawei from the country's 5G rollout.
Senator Payne said on Wednesday she would continue to monitor arrangements made with foreign nations, and she expected "the overwhelming majority of them to remain unaffected".
She said she had also approved a proposed memorandum of understanding between the West Australian government and Indonesia in regards to a minerals project.