At around 4pm a man was reported to have left a fast food restaurant on Low Road in Hunslet with a weapon concealed within his clothing.
He entered a small white van heading in the direction of the city centre and was stopped by armed police on Great George Street.
Two men aged 33 and 20 were arrested and are currently in police custody.
A search of the vehicle has been conducted, however no weapons have yet been recovered.
Police said that enquiries remain ongoing.
Buses were diverted on the Headrow due to the police response.