The ministry said since investigations such as these required complex testing, it was too early to say how long this may take.
Signs have been put up on the Ngunguru foreshore advising people not to take or consume shellfish from the area until results of the investigation was known.
Paratene Te Manu (Sonny) Wellington, kaumatua at the Ngunguru marae, said overfishing and silt accumulated over the years in the estuary have impeded the good growth of pipi and tuatua.
"In fact the marae committee has been working on putting a rahui for say five years to let the natural growth of these species to take place because the situation has become quite serious over the years."
He was not aware of the investigation until contacted by the Northern Advocate yesterday.
Mr Wellington said a build up of population also contributed to a scarcity of seafood.
"The fact is there's not enough shellfish there to cope with a large number of people. There was a time when you could go down there and get enough within a short time," he said.
Bob Patel, owner of Ngunguru Food Mart situated just across the road from Ngunguru foreshore, said the sandspit and estuary were used on an almost daily basis, particularly in summer.
"We've got to protect the sea and the locals are very concerned about it," he said.
MPI has urged the public to report unusual number of dead or dying animals, including fish and shellfish, to its exotic disease and pest hotline (0800) 80 99 66.
-Anyone with health concerns relating to shellfish in Northland beaches should contact the NDHB's on-call health protection officer on (09) 430 4100.