"One hundred twenty-eight people were suspected to be aboard the boat, but only nine bodies have been recovered, while there were two survivors so far," Yushau Shuaib, spokesman for the National Emergency Management Agency, told AFP.
He said the sinking occurred about two or three days ago some 40 miles (60 kilometres) off the coast of the southern city of Calabar, but that there was still some confusion about the origin of the boat.
Shuaib said he had been informed that the two survivors were rescued on Monday, but that their conditions so far had prevented authorities from speaking to them in detail.
There were indications that the boat had originated from Congo-Brazzaville, but that has not been confirmed, he said, without giving further details.
Such accidents at sea occur regularly in parts of Africa, with rickety boats often overloaded with passengers and few reliable records of who was aboard.
A rescue source speaking on condition of anonymity said initial indications were that the two survivors were Togolese.
A spokesman for the emergency management agency in Cross River state, where Calabar is located, said the wreckage of the boat had not yet been located.
The survivors were rescued by a patrol team from Addax Petroleum, a Chinese company which has operations in the oil-rich country, said the spokesman, David Akate.
The survivors are "yet to be stabilised," he said, but could not give further specifics on their condition.
Akate also said the boat had an estimated 128 passengers and that nine bodies had been recovered.
"We are still collating information on the mishap because it happened on the high seas," he said.
"We have not been able to get information as to where the boat took off from, where it was going and the type of boat. The accident happened at the weekend and the rescue operation started on Sunday."
In July 2012, a ferry sank in choppy waters as it crossed from mainland Tanzania to the island of Zanzibar, leaving at least 104 people drowned. Zanzibar authorities charged three people with manslaughter over the sinking of the ship, the MV Skagit, including its owner and captain.
In September 2011, more than 200 people perished when the MV Spice Islander, which the authorities admitted was overloaded, sank while sailing between two of the main islands in the Zanzibar archipelago. Rescue workers saved 619 passengers.
At least 50 people drowned and some 35 were reported missing after a boat accident on a river in the northwest of the Democratic Republic of Congo in July 2011.