Singapore's government said the suspected leader of the Singapore wing of the al Qaeda-linked Jemaah Islamiyah terrorist group is back in its custody two-and-a-half years after a daring jailbreak.

The Home Ministry said Mas Selamat Kastari is "currently under investigation" and being held under the country's Internal Security Act, which allows for detention without trial. Malaysian police deported the suspect Friday—nearly 18 months after capturing him in southern Malaysia.

Mr. Kastari escaped from prison in 2008—embarrassing tightly policed Singapore—by squeezing through a bathroom window at its Whitley Road Detention Center. Mr. Kastari spent 12 months on the run, evading a massive manhunt and raising fears that he was receiving support from a network of terrorist operatives across the region.

Malaysian police tracked down Mr. Kastari, who is of Indonesian descent, in Johor state in April 2009 and held him for interrogation until Friday, when authorities handed him back to their Singaporean counterparts. Singapore praised the cooperation on the suspect's transfer, which came on the heels of bilateral talks between Malaysian Prime Minister Najib Razak and Singapore's Prime Minister Lee Hsien Loong.

Singaporean authorities accuse Mr. Kastari, who is in his late 40s, of being the chief of the Singapore wing of Jemaah Islamiyah, the group responsible for the 2002 bombings in Bali, Indonesia, which killed 202 people, as well as a slew of other attacks. Officials say Mr. Kastari hatched a plan to hijack an aircraft and crash it into Singapore's Changi airport, one of the busiest terminals in the region.