The moves come amid a drive by both countries against armed groups operating in the troubled southern islands of the Philippines and the waters off Malyasia's neighbouring Sabah state on Borneo island.
Malaysia's army chief General Mohamad Azumi Mohamed said after a meeting here with Philippine army commander Lieutenant General Efren L. Abu that the field exercise would take cooperation beyond the current exchange programmes involving senior officers to involve personnel at a lower level.
The agency gave no details of when or where the exercise would be held.
Mohamad Azumi said they had also agreed to station liaison officers in Zamboanga City in the southern Philippines and in Kota Kinabalu, capital of Malaysia's Sabah.
"These officers will link both armies in sharing intelligence as well as to coordinate joint operations, mainly in the southern Philippines and waters off Sabah," he said.
The southern Philippines has been plagued by Muslim separatist violence by the Moro Islamic Liberation Front, and Muslim Malaysia has offered a neutral venue for forthcoming peace talks as well as ceasefire monitors.
Abu said the Philippine army was grateful for Malaysian assistance, especially in combating armed groups.
Mohamad Azumi said the monitoring team would be based in Cotabato City in the restive Philippine island of Mindanao for a year.
The team, which Mohamad Azumi said was likely to leave in one or two weeks' time, will comprise 51 army officers, five police officers and another four foreign ministry officials.