Victoria Police acting commander Tim Tully said more than 50 arrests had been made after clashes broke out between activists and officers.
"The majority of offences relate to obstruction of a footpath or intentionally obstructing an emergency service worker," he said.
Acting commander Tully said two people were arrested in relation to animal cruelty offences, after they allegedly assaulted a police horse brought in to control the crowd.
He said four officers were injured during the clashes, and two have been taken to hospital for treatment for finger and head injuries.
Another woman was also taken to hospital after she was allegedly trampled by a police horse.
"The only information I had was she was allegedly injured by a police horse, whether she was trampled or kicked, I’m not sure," acting commander Tully said.
A male was treated at the scene for a minor laceration to his head, he added.
Video posted to social media showed a number of police officers confronting protesters, while a number of activists who said they were protesting peacefully, complained of heavy-handed tactics from the police.
Other videos appear to show police using capsicum spray on protesters, who responded by chanting "we have a right to demonstrate, this is not a police state" and hitting them with batons.
Deputy Prime Minister Michael McCormack urged the media not to cover the protests because the activists crave "publicity".
"They absolutely want to have their Facebook and social media statuses updated by this sort of thing," he told the ABC.
"Mining and resources provide a lot of money, particularly for the welfare payments that a lot of those people are no doubt on."
The International Mining and Resources Conference is Australia's largest annual industry event and attracts delegates from the resources, investing and technology sectors.
More than 7,000 delegates from about 100 countries are attending the three-day conference.
Organisers said the protest action is based on misconceptions about the mining industry.
"There is a misconception that as an industry mining does not operate with sustainable principles in mind," conference organisers said in a statement.
“We work in an inclusive industry and we welcome a diverse spectrum of views at the forum. This includes the right of groups and individuals to make their views known through a peaceful protest outside the forum, but not to cause disruption."
Mining is vital for the production of electricity, solar panels, electric car batteries, pacemakers and medical apparatus and public transport, they added.
This year, the conference will consider the importance of battery minerals, used in the emerging electric car market, and the growing importance of ethical investment for resource companies.
Additional reporting: Abbie O'Brien, AAP