"The threat is real and we are not immune to it... we must recognise that no security system can be completely foolproof."
Singapore, the world's busiest container port, lies at the southern end of the strait which acts as one of the world's key maritime arteries linking Asia with the Middle East and Europe.
More than 50,000 merchant ships transit the 900-km long strait every year carrying about 40 per cent of the world's trade.
On Thursday Singapore, Malaysia and Indonesia, who are jointly responsible for securing the waterway, said they had stepped up maritime and air patrols over the straits.
Wong did not specify who might be behind the threat, but the alert comes after police in neighbouring Indonesia conducted a series of raids in northern Aceh province.
Officials said 14 people had been arrested in the raids, accused of plotting terrorist attacks.
In one raid on Thursday a fierce gunfight broke out, killing a police officer and injuring 10 others.
In December 2001 Singapore police said they had uncovered a plot by the Jemaah Islamiyah (JI) group to attack multiple targets in the city, including the US embassy.
JI, which has been blamed for a string of attacks across Southeast Asia, has been linked by US and regional intelligence agencies to al-Qaeda.