He gave no other details of the operation.
Earlier, Singapore media reports said the suspected commander of JI Singapore was detained in early April in a joint operation involving security agencies from both countries.
Mas Selamat, 48, escaped from a tightly guarded detention centre in February last year after squeezing through a toilet window that had no bars and climbing over a fence.
The government subsequently sacked or disciplined nine officials over the incident.
|Mas Selamat's escape led to a huge manhunt and a global alert from Interpol [EPA]
Singapore's Straits Times
newspaper, quoting "senior intelligence sources", said Mas Selamat was captured on April 1 in Malaysia's southern state of Johor, just across the causeway from Singapore.
It is believed he is being held for interrogation by Malaysian authorities under the country's own internal security law, which allows for indefinite detention without trial.
His escape sparked the biggest manhunt in Singapore's history and a global security alert from Interpol.
Mas Selamat is alleged to have masterminded a plot to hijack a plane in Bangkok and crash it into Singapore's Changi airport about six years ago.
Singapore authorities have also accused him of planning truck bomb attacks at several sites across the island state, including the American Club and US Embassy.
Mas Selamat had been held under Singapore's Internal Security Act and had not been formally charged with any crimes at the time of his escape.
Rohan Gunaratna, the head of the International Centre for Political Violence and Terrorism Research at Singapore's Nanyang Technological University, said Mas Selamat was "an escape artist", having escaped twice in Indonesia previously and once from Singapore.
"JI still poses a very significant threat ... it is the pre-eminent terrorist group that is active in southeast Asia"
Rohan Gunaratna, terrorism analyst
"On all three occasions he was arrested by the Indonesian, and this time by the Malaysian authorities, based on the co-operation extended by Singapore intelligence," he told Al Jazeera.
Gunaratna said authorities in Singapore and Malaysia delayed the announcement of Mas Selamat's arrest because they needed time for further investigations.
"Mas Selamat operated with a terrorist network and his associates had to be watched and interrogated," he said. "They needed more time to interrogate him and his associates."
Mas Selamat, Gunaratna said, was one of the "most dangerous and determined" terrorist whose arrest is a "very significant victory for governments in this region".
"JI still poses a very significant threat. In fact it is the pre-eminent terrorist group that is active in southeast Asia," he said.
JI has been blamed for a string of attacks across southeast Asia, including the Bali bombings that killed more than 200 people, many of them foreign tourists.