Police say a 31-year-old man was hit while on the B12 bus at East New York Avenue and Thomas S Boyland Street in the Bronwnsville section just before 10 a.m.
Witnesses said the victim was arguing with another man and then shoved him. The other man responded by opening fire.
The victim was shot in the left hand. He was taken Brookdale University Hospital with a non-life threatening injury.
The other man, a 47-year-old, was taken into custody. He was being questioned, but no charges were immediately filed.
The gun was recovered on the bus.
No other passengers were hurt.
As a result of the police investigation, B12 buses are detoured.