Protected seals, whose carcasses were found along Co Down shores, were decapitated and possibly shot, the Northern Ireland Environment Agency says.
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In total, 16 seal carcasses were recovered from Strangford Lough, Minerstown and Dundrum Bay between late June and the end of November 2009.
Twelve had suffered an unnatural death, with evidence of gunshot wounds, knife cuts, drowning or broken jaw.
In 2008, post-mortems showed four seals had their heads removed by a sharp blade.
Five other suffered from an unnatural death that year.
One seal was found with a net caught around its neck, although there was no evidence of legitimate licensed fishing activity.
Declan Looney, Senior Wildlife Inspector with the NIEA, expressed concerns over the high number of unnatural seal deaths along the Co Down coast in the past two years.
"Both harbour and grey seals are species protected under European and Northern Ireland legislation.", he explained.
Experts don't know who is responsible for the deaths.
"We're asking the public for their support in helping us to solve this mystery", Mr Looney told UTV.
"They appear to have drowned first. They appear to have become trapped in some kind of net and the heads have been cut off to get them out of whatever they were caught in. We don't know what they were caught in."
He said post-mortems found no evidence linking the deaths to the marine current turbine being trialled in the Strangford Narrows, "as this would not inflict the sharp cuts seen.
"The Agency accepts that some deaths by drowning may be the result of inadvertent by-catch in legitimate fishing nets. The reporting of such instances will help evaluate the scale of this problem and assess ways of minimising this risk".
Mr Looney urged members of the public to report all dead seal stranding to NIEA on 028 4461 5520.
"Anyone who witnesses suspicious activity involving seals should report this immediately to their local PSNI station", he said.
© UTV News