Vets say dozens of dogs have fallen ill, with vomiting and diarrhoea, after walking along the coast in recent weeks.
But environmental health experts from councils in the area claim that dogs who have not visited beaches have also fallen ill.
They are working with the Animal and Plant Health Agency to establish the cause of the mysterious illness.
Kirsty Salisbury, general manager of Coastal Services for East Riding of Yorkshire Council, said: “From reports from local veterinary surgeries, the illness they are seeing within dogs and the tests carried out have not provided any direct links with the use of beaches.
“We would advise that, if your pet becomes unwell and has continuing sickness and diarrhoea, you should make an appointment to have your pet seen. It appears that many dogs are becoming unwell even though they have not visited beaches, so it may be that this is a general illness amongst dogs.
"Our Coastal Services team regularly inspect the beaches for signs of any irregular occurrences and at present there is nothing unusual; however, this will continue to be monitored and action will be taken, if and when necessary.
“We encourage people to be aware and mindful, and if they are on the beach, or anywhere, not to let their dogs off the lead, so that owners can see what the dogs are picking up and potentially eating.”
A Scarborough Borough Council spokeswoman said: “The cause of the illness, and the locations it appears to be linked to, are unclear.
“While dogs walked on beaches have been affected, we have also read reports from dog owners that the same symptoms are affecting dogs only walked at inland locations away from beaches.
“We are in discussions with our partner organisations to gather intelligence and carry out investigations into possible causes.
“If any vets have information about possible links to a canine virus that could help these investigations, we kindly ask them to contact our dog warden service.”
The Environment Agency has said there is no evidence to suggest this illness is linked to the incident in October, which saw thousands of dead crabs and lobsters wash up along the North East coast.
Investigations found the crustaceans had not been killed by chemical pollution, undersea cabling, seismic survey activity or dredging.