A controlled explosion was carried out on a car in the cemetery on the Lone Moor Road in Londonderry shortly before midnight on Wednesday.
Searches were carried out on Thursday morning but nothing further was found.
Supt Mark McEwan said the guns are being linked to violent dissident republican activity.
He said he was thankful that the weapons were now out of circulation.
"This is a sensitive area to carry out these operations and shows the disregard for the community on the part of those involved in this type of activity," he said.
"In the district, this is the third firearm we have taken out of circulation this week.
"These are weapons that are made and possessed with one purpose in mind and that is to kill or cause serious injury to people."
A security alert at Derry City Cemetery, that led to the discovery of two semi automatic handguns, has ended.