Fill small nail holes with silicone caulk or roof cement.
How to seal roof nails.
Smaller nail holes will be permanently fixed by this method standard roofing nails would be either 3 8 inch or 1 2 inch making a hole.
Remember to seal over the nail heads.
Some roof leaks are tough to locate.
Make sure the roofing cement extends to each side of the nail head covering it completely.
Remove nail lift shingle and apply a small dab where nail penetrated shingle then push the overlapping shingle down and your done.
Apply a glob of roofing cement to the spatula or putty knife.
I ve always considered it necessary to caulk any exposed nail heads on a shingle roof there shouldn t be many.
Alternatively or in addition you can drive a new nail nearby for a fresh stronger hold into decking.
Wipe the glob of roofing cement over the nail head.
Don t worry if the glob looks a bit thick.
For loose nails that have yet to push through shingles you can lift up the shingle and hammer the rising nails back down.
The nails might have popped.
I heard an opposing opinion recently.
The claim was that nails have to pass through a minimum of two layers of shingles.
The shingles are asphalt backed and this asphalt forms an adequate seal around the nail.
It will smooth out once it dries.
They are electro galvanized to help resist rust and corrosion.
I must admit i ve seen many builders that do not seal the nail heads.
Roofing nails sticking up called nail pops might look like an unimportant issue.
If your ceiling has a plastic vapor barrier between the drywall and the attic insulation push the insulation aside and look for flow stains on the plastic often water runs to openings in the vapor barrier such as at ceiling light fixtures.
I would suggest to remove the nail and put a urethane sealer which can be found at any home store to seal the hole from underneath.
They can also be used to apply insulation board and felt to wood substrates.
However they can cause leaks particularly if you have an asphalt shingle roof.