The state will also help pay for horse owners to bring horses stranded in flu-affected New South Wales and Queensland home.
The $A1.94 million was announced by Premier John Brumby, who said the extra funding will assist recreational horse owners who are ineligible for assistance under the federal government's flu package.
"This new funding will allow us to meet short and long-term priority objectives which have been identified and requested, in consultation with the industry," he said.
The funding, to be administered by the Department of Primary Industries (DPI), includes:
Mr Brumby said many non-racing horse associations had done a tremendous job in keeping equine flu out of Victoria and he appreciated the ongoing support of associations who voluntarily cancelled events and reduced the risk of spreading the disease.
"I thank every Victorian horse owner for co-operating with existing border controls and implementing biosecurity measures," he said.
"The Government is very aware of the impact the voluntary cancellation of events has had on non-profit clubs and associations when the competition season was just getting under way.
"I'm confident that this additional funding will help Victorians meet any challenges that lie ahead.
"Since the outbreak of equine influenza, the Victorian Government has committed $2.4 million to assist the State's non-racing horse owners."
The state government has also launched the second phase of an information campaign aimed at keeping Victoria free of flu.
Key elements include regional TV and radio advertising, a targeted media campaign focusing on major horse activity areas, billboards urging people 'Not to cross the line' and letters to 18,000 horse owners.
Last week saw the first repatriation, of 46 recreational horses, from New South Wales and Queensland since the EI outbreak.
"DPI has worked within the new nationally agreed protocols to assist owners in returning their horses from disease free Green Zones and a significant slice of the funding will be set aside to subsidise this project," Mr Brumby said.
"While the number of horse flu cases reported from interstate is abating, there is still a risk of the disease entering Victoria and it is vitally important that horse owners remain vigilant to keep Victoria EI free. I urge all horse owners to continue to implement appropriate biosecurity procedures when in contact with horses."