Smugglers were arrested in Malaysia on Wednesday with some 3,300 endangered turtles aboard their boat, officials said, as the country battles to clamp down on the burgeoning illicit wildlife trade.

Malaysia has in recent years developed a reputation as a transit point for trafficked animals. This haul comes two weeks after authorities seized a record 30 tonnes of pangolins and their scales.

The two unidentified smugglers were stopped by the coastguard just after midnight off the southern state of Johor.

"Seven packages containing about 3,300 turtles were believed to be... brought in to be sold in the country," senior coastguard official Commander Mohammad Othman said.

The seized turtles were estimated to be worth about 150,000 ringgit ($37,000) and the case is now being handled by wildlife officials, he said in a statement.

Othman did not say where the smugglers might have come from.

The animals were identified as the pig-nosed turtle, a freshwater species classified as "endangered" by The International Union for Conservation of Nature (IUCN), and found in the south of Indonesia's Papua and Papua New Guinea as well as in northern Australia.

The species is in high demand in Singapore and China, where they are sold as exotic pets and sometimes end up in food markets.

Wildlife trafficking watchdog Traffic Southeast Asia called the number of turtles seized "incredible", adding that it was a big concern for the species, which is only found in a limited area and is heavily threatened by trade.

"There is a need to look into whether there is a demand for these pets here and whether it would be sent further on to other markets," said the group's senior communications officer Elizabeth John.

"We hope the investigation into the case leads to more intel on smuggling patterns from Indonesia and neighbouring countries," she said.