Environmental experts and forest officials had feared negative effects after a tanker carrying over 350,000 litres of furnace sank in the Shela River on Tuesday.
Oil spread to 34,000 hectares in three days, causing seven four-month-old crocodiles to fall sick, the officials said.
Sore mouths were spotted in them in salt water reservoirs at the reproduction centre, located at the Chandpai range on the bank of Pashur River of the Sundarbans east zone, on Thursday.
The wildlife reproduction centre forest ranger Abdur Rab on Thursday night told bdnews24.com: "We changed the water of the crocodile's salt water reservoirs when tidal water came at river Pashur on Tuesday afternoon. The rising water, that contained oil, entered the reservoir."
"So, we didn't replace the reservoirs water with water from the Pashur River since that day. But today I spotted sore mouths on 'Pilpil' and 'Juliet's' seven babies, who were born in last August."
They were already under treatment, he said.
The water of the reservoirs used to be changed every day. But it has been temporarily stopped because of the oil spill in the river.
"The crocodile babies are living in their wastes due to the unchanged water. If the situation persists, they have to be moved somewhere else," Rab said.
The forestry official thinks their infection was caused by the oil-contaminated water.
The Sundarbans East Division Forest Officer (DFO) Md Amir Hossain Chowdhury said there are 255 four- to six-month-old salt water crocodiles in 18 reservoirs at the Karamjal Wildlife Reproduction Centre.
The country's only crocodile reproduction centre, east Sundarbans Karamjal Wildlife Reproduction Centre, was established in 2002 under the Sundarbans Biodiversity Conservation project over eight acres of land with an expenditure of Tk 3.2 million.
It started with five crocodiles of various sizes which were caught by fishermen in different rivers. The centre is overseen by forest official Rab who was trained at Australia's International Wildlife Conservation Centre.
Wildlife experts have expressed grave fears over the fate of Irrawaddy dolphins after the oil-filled tanker sank after being hit by another cargo vessel around the rare dolphins sanctuary.
The dolphins sanctuary lies in rivers Shela and Pashur of the Sundarbans, covering an area of 31 sq km. The Karamajal Wildlife Reproduction centre, on the bank of river Pashur, is their free roaming area.
But no dolphins were seen jumping in the water on Wednesday and Thursday, Karamjal officer Rab said. The marine creatures will not survive this, they'll go away, he feared.