A species thought to be an invasive sea squirt which can smother native organisms has been discovered on the bed of Strangford Lough, the Environment Agency said.
Samples from a recent survey of marinas are causing concern amongst marine experts in Northern Ireland.
A senior scientist from the Countryside Council for Wales has been asked to undertake dives and advise on how to manage the threat from the Japanese organism.
Its identity is still being confirmed but it could threaten native marine habitats and species while interfering with fishing because of its suffocating nature.
Environment Minister Alex Attwood said: "I am concerned about this. It is particularly hard to prevent invasive species spreading in the marine environment and even more difficult to control them once they are there.
"The possible presence of Didemnum vexillum (carpet sea squirt) adds a new challenge to managing Strangford Lough which is so important for its marine life."
The invasive carpet sea squirt is believed to be native to Japan, where waters are similarly temperate. It can hang from any hard surface like docks, lines and ship hulls or form mats on seabeds.
It is an offence to release the squirt into the wild or cause its further spread. It can spread through larvae or fragmentation but is mainly transported over longer distances on boat hulls, fishing equipment and nets.
If confirmed this would be the first record of Didemnum vexillum for Northern Ireland, having previously been recorded in the Republic of Ireland, the south coast of England, Wales and Scotland.
The find was made by investigation experts.
The Northern Ireland Environment Agency has invited Dr Rohan Holt, a senior scientist from the Countryside Council for Wales and expert on the survey and eradication of Didemnum vexillum, to dive suspected locations in Strangford Lough and advise the Agency on possible management measures. It is hoped these dives will take place next week. In Holyhead, Wales, control works are expected to cost more than £500,000.
Island-studded Strangford Lough is the largest sea inlet in the British Isles, covering 150 square kilometres. It is a popular tourist attraction noted for its fishing. It is a conservation area and its wildlife is recognised internationally for its importance.
The Agency is encouraging all coastal water users, especially in Strangford Lough, to report possible sightings with photos through the "alien watch" facility of the Invasive Species Ireland website. Members of the public are urged not to remove them from vessels and structures in the sea as fragments can survive and be carried to colonise other locations.
Mr Attwood said he was establishing a working group to agree on appropriate actions in response to this potential threat.
"I will be ensuring that those actions take place as a matter of urgency and I will be keeping a very close eye on this," he said.
An all-Ireland workshop on invasive species is to be planned in the near future.