But officers discovered a sawn-off shotgun close to where the cars were abandoned.
The area was cordoned off after police arrested two men seen acting suspiciously in the Mullaghbane Road area of the city on Wednesday night.
The alert continued on Thursday until the all-clear was given at about 1500 BST.
The cars were taken away for examination while the police continued to question the two men.
It is understood they were arrested under anti-terrorist legislation.
Meanwhile, a security alert in County Tyrone has turned out to be a hoax.
A number of houses in the Mount Sion area of Strabane were evacuated during the alert which followed the discovery of a suspicious package in the Ballycolman estate.
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