The fishing vessel went down on March 5, prompting rescuers to comb waters off southern Sindh province with helicopters, ships and speedboats, the AFP reported.
"The bodies of 12 fishermen have been recovered," the army public relations wing said in a statement on Wednesday.
"The search for the remaining two missing fishermen is still going on."
Deadly transport accidents are common in Pakistan, where overcrowding is rife and safety measures are lax.
The military earlier said the boat had 45 crew aboard when it overturned in the open sea near Hajamro Creek -- close to the Indian border -- "due to adverse weather conditions".
Leisure boats and working vessels in Pakistan are frequently overloaded, making them top-heavy and susceptible to capsizing, according to the AFP.
MNA