But some biologists say the plan is impractical and unlikely to succeed, since no reptile is ever known to have been cloned.
The Fisheries Department hopes to embark on a leatherback cloning project that could cost 32 million ringgit (US$9.28 million; EUR6.75 million) over five years, said its director-general, Junaidi Che Ayub.
"The number of leatherbacks is decreasing every year," he told The Associated Press. "Even though some of them have returned to our shores to nest, their eggs are not fertile and do not hatch." He did not say why.
"Cloning is just a proposal," he said. "We have to be creative and innovative, we have to think of many ideas."
Junaidi said the clones could produce hatchlings to boost the population.
Malaysia once had one of the world's largest populations of the turtles, which returned regularly to its east coast beaches to lay eggs. Overfishing and pollution have sharply cut their numbers.
A United Nations report last year said leatherbacks - which can weigh up to a ton - have become virtually extinct in Malaysia, with nest sites dipping from 5,000 in the 1960s to less than 10 in recent years.
Junaidi said experts from the department are working on a detailed proposal, which includes studying Malaysia's cloning policies, before submitting it to the government for approval. No known animal cloning has yet been done in the country.
Tests could first be carried out on Malaysia's abundant green turtles to see if cloning is workable, he added.
However, some biologists said cloning is unfeasible and a waste of resources.
"It's a bizarre idea," said conservation biologist and university lecturer Chan Eng Heng.
Cloning has been done only on mammals such as dogs, sheep, cats and cows - and uncertainties persist about cloned animals' health and life spans, she told the AP.
"The money can be used to carry out other conservation work that will really make a difference," she said.
Malaysia's waters are visited by four turtle species - the Olive Ridley, the leatherback, the green and the hawksbill. All are listed as endangered or threatened with extinction. Human activity, including shoreline development, fishing, pollution and the stealing of eggs has increasingly threatened the creatures.
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