Influenced by Christchurch killer Brenton Tarrant, the teenager had allegedly planned to knife his victims and livestream the attack.
He is the youngest to be detained under the Internal Security Act, which allows for detention without trial.
The Christchurch attack was the worst mass shooting in New Zealand’s history.
Some 51 people died when they were gunned down by Tarrant – who has now been sentenced to life imprisonment without parole – at two mosques on 15 March 2019.
The 16-year-old Singaporean, who has not been identified but has been described as a Protestant Christian, is said to have been “motivated by a strong antipathy towards Islam and a fascination with violence,” said the country’s Ministry of Home Affairs (MHA).
He is the first detainee to be allegedly inspired by far-right extremist ideology in Singapore, where terror attacks and violent crimes are rare. The boy has been in detention since last month.
The ministry said that it was clear he had been influenced by Tarrant, pointing out the fact that he planned to carry out his attacks on 15 March this year, to mark the two-year anniversary of the Christchurch attacks. He had also allegedly confessed that watching Tarrant’s livestreamed attack had given him “a rush”.
He allegedly planned to attack two mosques – Assyafaah Mosque and Yusof Ishak Mosque – both of which were near his home.
The boy had intended to steal his father’s credit card to rent a car and drive between the two attack sites, situated in the north of the island. He had no driving license, but was confident he could “make it work”, said officials from the Internal Security Department at a briefing.
The teen had allegedly originally planned to use a rifle like Tarrant, but decided to use a machete instead after he encountered difficulties in purchasing a firearm in Singapore, which has strict gun-control laws. The ministry added that he appeared to act alone.
Officials also said he prepared documents which he intended to disseminate before his attacks, one regarding the Nice attacks last year, and the other a manifesto detailing his hatred for Islam, in which he expressed hope that his intended attack would be called a “justifiable act of violence”.
Authorities said they received a tip-off in November, and arrested him soon after.
The MHA said during interrogations the teenager admitted that he could only “foresee two outcomes – that he is arrested before he is able to carry out the attacks, or he executes the plan and is thereafter killed by the police”.
“He went in fully prepared, knowing that he is going to die, and he was prepared to die,” law and home affairs minister K Shanmugam told local media outlets.
Authorities said he will undergo “religious, psychological and social rehabilitation”, which will include engaging a Christian counsellor to “help him correct the radical ideology he has imbibed”.
Mr Shanmugam said the case was a “worrying development”, noting that several youths under the age of 20 have been held or given restriction orders under the Internal Security Act in recent years.
Authorities have previously detained suspected Islamist extremists, including a 17-year-old.
