A spokeswoman for the shipping firm said the Mogamikawa had been heading for Singapore, but would now stop in the United Arab Emirates to check the extent of the damage.
Commander Kevin Aandahl of the US Fifth Fleet based in Bahrain confirmed that "an incident took place between one of our subs and a Japanese merchant ship".
The Japanese government has asked the US to investigate the cause of the collision.
The Newport News is based in Groton, Connecticut, and was launched in 1986. It has a crew of 127.
In February 2001, a US navy submarine rammed into a Japanese fishing vessel in waters off Hawaii, killing nine people. The American captain's delay in apologising for the crash brought protests from the victims' families.