In an idea that seemed to come straight out of a James Bond film, Budi Waseso this week unveiled the prison island plan, explaining that crocodiles can't be bribed by drug traffickers seeking to escape jail.
He embarked on a tour of the country to find "the most ferocious type of crocodile" to guard the jail, which is to be for drug convicts who have been sentenced to death.
"It is also possible we may use piranhas, and because the number of personnel at the prison might not be enough, we can also use tigers," he was cited as saying in local reports.
Indonesia already has some of the toughest anti-narcotics laws in the world, including death by firing squad for traffickers, and sparked international uproar in April when it put to death seven foreign drug convicts.
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Despite the harsh laws, Indonesia's corrupt prison system is awash with drugs, and inmates and jail officials are regularly arrested for narcotics offences.
Anti-drugs agency spokesman Slamet Pribadi confirmed Waseso was also weighing the possibility of tigers and piranhas as guards, and hit back at suggestions the prison island plan was a joke.
"This is serious, this is not a joke," Pribadi told AFP.
"Drug trafficking is an extraordinary crime and therefore the fight must also be extraordinary, we cannot fight the usual way."
The plan has echoes of the Bond movie "Live and Let Die", when the secret agent escapes from an island surrounded by crocodiles by using the reptiles as stepping stones.