The government established an emergency zone along about 100 km (60 miles of coast) and had asked people to avoid swimming and fishing.
The ship had been carrying almost 200 tonnes of ammonium nitrate used in fertilizers and explosives.
But a spokesman later said only small traces had been found in the water.
Costa Rica's Emergency Commission said bathing was considered safe but fishing would be banned for a further 72 hours.
Reinaldo Carballo said the emergency alert had been considered preventive "because of the potential impact ammonium nitrate could have on human health".
He said they hoped the chemical, which is highly soluble, had dissolved and been taken out to sea on the tide.
Government officials said an enquiry into who was responsible for the ship sinking and the spillage would begin as soon as possible.
Costa Rica has the largest number of foreign tourists in Central America and is a popular destination for nature and eco-tourism because of its pristine beaches, tropical forests and large nature reserves and parks.
A ship containing toxic chemicals sparked an emergency alert off the coast of the Costa Rica tourist town of Puntarenas when it sank in heavy seas.