To fix a metal flashing leak it is important to have a professional roofing contractor inspect the flashing to see if it needs to be replaced or resealed. To repair the flashing area purchase polyurethane sealant and a caulking gun. It is important to apply the polyurethane sealer to a dry and clean surface. Remove any dirt and debris from the flashing joint prior to sealant installation. Using a quality caulking gun apply steady pressure force the sealant into the joint. It will take a couple of days for the sealant to fully cure.