The protest at Port Botany in Sydney's east started about 9.30pm on Sunday with Maritime Union of Australia (MUA) activists saying it was a "peaceful community assembly" at one of the terminals.
Hundreds of protesters took part to demand state and federal governments exclude Israeli company ZIM from Australian ports and implement broader sanctions on Israel.
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The group says the Israeli company is complicit in the war in Gaza.
But 15 minutes after the protest began, the union said "police moved in and started assaulting and arresting demonstrators".
Among those arrested included MUA branch secretary Paul Keating, organiser Shane Reside and other delegates, the union said.
NSW Police confirmed 19 people had been arrested and charged at the protest.
Officers said they responded to the "unauthorised protest" at Port Botany at 6.50pm before the group moved to Penhryn Road and blocked the road and access to the port.
"The crowd was directed to move from the roadway, and given some time to do so," NSW Police said in a statement.
"A number did not comply, and were arrested for disobeying police direction."
All 19 people arrested were charged with obstructing a driver or pedestrian's path, failing to comply with a move along direction and remaining near a major facility causing a serious disruption.
They are expected to appear in court on Wednesday, May 8.
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