A number of homes were evacuated on Monday following the discovery of a number of “suspicious items” in the Fahan Street area around 11 am.
Army bomb experts carried out searches and a cordon was extended to the city walls on Monday afternoon.
The security alert is ongoing but police have not yet release details of what sparked the clearance operation.
The PSNI said 13 households had to be evacuated during the security alert.
It said its primary aim throughout the operation was to keep the community safe.
During the security operation on Monday night, police said they also had to “deal with disorder in the Fahan Street area of Derry”.
At 1 am on Tuesday morning, police said: “The area is now calm.”
The PSNI say a number of police vehicles were damaged after missiles were thrown at them.
Derry City and Strabane Area Commander, Chief Superintendent Ryan Henderson said: “It is extremely disappointing to have witnessed the scenes of disorder on our streets last night.“Our officers have been in the area following the discovery of a number of suspicious items yesterday morning and we have been working to ensure the area is made safe.
“Scenes like those on our streets last night are senseless.
“Thankfully, we were able to bring the situation under control and restored calm to the area.
“I want to thank everyone who has been affected by this incident.
“I know how disruptive it has been, especially for residents who had to leave their homes.
“Our primary aim throughout the course of this operation is to keep our community safe.
“We are working through this situation as quickly as we can.
“Everyone’s safety is our top priority and we will not take any risks with that.”
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