US Homeland Security Secretary Chad Wolf has said federal agents "will not retreat" in their efforts to protect government buildings in Portland.
"If you are a violent rioter looking to inflict damage to federal property or law enforcement officers, you need to find another line of work," he said.
US President Donald Trump sent officers to Portland to protect federal property amid anti-racism protests.
But the mayor of Portland has called for them to leave the US city.
There have been nightly protests against police brutality in Portland since the death of George Floyd, an unarmed black man, in Minnesota in May.
In recent days, however, violent clashes between demonstrators and federal law enforcement officers have escalated.
What did Chad Wolf say about the violence?
Speaking during a press conference on Tuesday, Mr Wolf said federal law enforcement officers in Portland were only targeting and arresting demonstrators who had been identified as being involved in "criminal activity".
He said the department respected the right of people to protest peacefully, but urged demonstrators to "please do so away from the violent activity taking place near the courthouse on a nightly basis".
On Monday evening, federal officers fired tear gas to disperse large crowds of protesters - some armed with hammers - who had gathered outside the city's courthouse and were throwing projectiles.
Mr Wolf also denied claims that the security officers had no identification and insisted they were wearing insignia showing they were police.
"These officers are not military, they are civilian police officers," he said, adding that they were required to restore order following "violent criminal activity every single night for 52 nights" and in response to "a lack of action from city officials".
"We will continue to take the appropriate action to protect our facilities and our law enforcement officers," he said, adding that federal agents will leave Portland when the violence stops.
What's been happening in Portland?
The last week has seen a violent escalation between protesters and federal agents, deployed two weeks ago by Mr Trump to quell civil unrest.
A report from Oregon Public Broadcasting (OPB) this week contained detailed accounts of witnesses who had seen federal law enforcement officers dressed in camouflage emerge from unmarked vehicles, grab protesters without explanation, and drive off.
Mr Wolf said on Tuesday that federal officers had arrested 43 people in Portland since 4 July.
At the weekend, fencing erected around the federal courthouse to protect the building was dismantled by protesters just hours after it was put up.
The prosecutor's office in Oregon said on Twitter that the fence aimed to "de-escalate tensions" between protesters and law enforcement officials and asked people to leave it alone.
Officers also declared that a riot had taken place outside the Portland Police Association building, which was set on fire.
What has the Trump administration said?
In a tweet on Sunday, President Trump defended the actions of the federal government.
"We are trying to help Portland, not hurt it. Their leadership has, for months, lost control of the anarchists and agitators," he said.
Earlier in the week, the president said officers in the city had done a "great job".
"Portland was totally out of control, and they went in, and I guess we have many people right now in jail," he said on Monday. "We very much quelled it."
Mr Trump has threatened to send federal law enforcement officers to control protests in other major US cities, including Chicago and New York.
The mayor of New York, Bill de Blasio, has said he will take the president to court if he goes ahead with his threat.