Defence Secretary Delfin Lorenzana says a Philippines air force plane spotted more boats than usual in a flotilla on Saturday.
Abdul Kadae, the suspect who was detained on Saturday, is the first person to be arrested in connection to the blasts.
President Duterte is scheduled to meet US President Barack Obama at a regional summit in Laos on Tuesday.
Authorities believes the suspect to be a part of the KGR@Katibah GR, a group headed by Gigih Rahmat Dewa.
The two nuclear-armed neighbours have been moving to gradually ease long-existing tensions between them.
Officials say some of the injured were rushed to hospitals in provincial capital Qalat as well as neighbouring Kandahar province.
The Singapore Embassy officials in Malaysia are assisting the families of those injured.
The train blast comes a day after the peace talks between Thailand's military government and Muslim separatists.
Authorities say the tremor was felt in Butuan and Cagayan de Oro, major cities in north-eastern Mindanao.
Authorities say Typhoon Namtheun was heading north towards the southern main island of Kyushu with gusts of up to 198 kmh.
The police say the accident took place at the junction of Bukit Panjang Ring Road and Bukit Panjang Road.
Authorities say this is the latest assault that has been targeted to the legal community of Pakistan.
The raid came six days after Bangladesh-born Canadian citizen, accused of masterminding the cafe attack, was killed.
Although no group has claimed responsibility yet but Duterte says it could possibly be a reprisal from extremists.
Separatists say that they would surely consider the creation of "safety zones" which is proposed by the Thai government.