About a pound of cocaine was also found at the house, the Belfast Telegraph reported.
Two men were arrested in the Thursday raid. One was was released on bail and the other was kept in custody.
Investigators had received tips about suspicious activity in the house.
A machine gun, two handguns and the cocaine were discovered in the attic.
Large loyalist demonstrations, many of them turning into bottle- and stone-throwing riots, followed a vote by the Belfast City Council in early December to limit the number of days the British flag is flown at City Hall.
The row house close to the center of Londonderry is adjacent to a loyalist housing estate but there was no suggestion the weapons were related to the political violence, police said.