Police officers in riot gear protected masked contractors who removed material from two bonfire sites in east Belfast.
A number of roads were sealed off near Bloomfield Walkway, and police also closed a section of the Albertbridge Road between Woodstock Link and Templemore Avenue.
Concerns had been raised over the safety of the Cluan Place and Bloomfield bonfires.
On Tuesday, a court ordered that the Bloomfield bonfire be reduced in size.
However, it was set alight in the early hours of Wednesday morning and missiles were thrown at police when they moved in to secure the site to allow contractors to remove material.
Bonfires are traditionally lit in many loyalist areas of Northern Ireland on the Eleventh Night - the eve of the Twelfth of July.
The fires mark William of Orange's victory over King James II at the Battle of the Boyne in 1690 and supporters say they are an important part of loyalist culture.
According to BBC News NI's Home Affairs Correspondent Vincent Kearney contractors were called in by the Department of Infrastructure after Northern Ireland's Fire Service raised concerns about the Cluan Place bonfire.
BBC News NI Reporter Mark Simpson at the scene.
The bonfire at Cluan Place has been cleared and the contractors have left the area.
A number of police officers remain at the scene but the Albertbridge Road has been reopened to traffic.
A small crowd has gathered at the entrance to Cluan Place where the bonfire had been built.
It took three hours to clear the bonfire. Contractors wore masks and drove vehicles with no number-plates.
At the nearby Bloomfield Walkway bonfire, contractors have finished removing material. A police presence remains at the scene.
Their assessment was that the buildings on either side would be destroyed if the fire was lit.
Sources say loyalists tried to light the bonfire when police vehicles moved in but officers extinguished flames and provided a protective cordon until contractors arrived.
It is understood loyalist community representatives in the area were made aware of safety fears but did not offer any assurances that the bonfire would be reduced in size or dismantled.
Bonfire built beside listed building
A historic listed building described as "making a significant architectural" contribution to the area was among the sites potentially threatened by the Cluan Place bonfire.
The bonfire was constructed just yards away from the former Ulster Bank building.
It was constructed between 1908 and 1910 and was listed as a historic building in 1987.
Information held by the Department of Communities website indicates that the building's upper floors were converted into office space while the "internal layout retains a partially-intact early 20th-century interior".
The building's online description adds that it also makes a "historic contribution" to the surrounding area.
Speaking to BBC News NI Assistant Chief Constable Alan Todd said there are 218 bonfire sites in Northern Ireland and the majority of them are responsibly organised.
"Unfortunately there are one or two exceptions and we've seen those day".
Mr Todd added that anybody who wishes to build a bonfire as a legitimate expression of their culture should engage with the landowner and agree on how the bonfire is to be managed.
Bloomfield Walkway Bonfire
On Tuesday a High Court judge directed the Department for Infrastructure to take immediate steps to reduce the size of the Bloomfield walkway bonfire to a maximum of 3m (10ft) as it was "out of control".
The ruling resulted from emergency proceedings brought by Belfast City Council amid claims the controversial 80-pallets-high construction posed a serious threat to surrounding homes.
The Bloomfield walkway bonfire was lit as police moved in to protect contractors who were due to remove materials from the site, according to the Police Service of Northern Ireland.
Vehicles were also set on fire in east Belfast.
In a tweet, PSNI Chief Constable George Hamilton said there was an unfortunate display of reckless behaviour at the Bloomfield walkway bonfire site on Wednesday morning.
He added that the "so called loyalist expressing their culture and tradition" were not reflective of the vast majority in east Belfast."
We are aware of speculation that contractors will be removing materials from other sites in and around the east of the city. This is not the case. The operations at Bloomfield Walk and Cluan Place are necessary to protect nearby buildings and residents who live in the areas.— PSNI (@PoliceServiceNI) July 11, 2018
The DUP MP for the area, Gavin Robinson, said his party supported the council's move for the court action and that those behind the bonfire left residents living "continually in fear".
He told BBC News NI that "sinister elements" involved in setting up the bonfire were risking the property and lives of people in the area.
"To my mind there is no part of unionist culture that involves the potential threat of burning out your neighbours, of destroying property or of risking life.
"Over the last number of years, people that live in the Bloomfield area feel for weeks before the Eleventh of July they live under a state of siege."
"People on the site lit the bonfire with total disregard for the safety of the local community and threw missiles at police," said Assistant Chief Constable Alan Todd.
"It is disappointing that some people decided to resort to violence as attempts were made to reduce a significant threat to the life and property of local people, due to the size and location of this bonfire."