"Our security operations continue, the only difference is that it may be less in scale and intensity," Lieutenant-Colonel Nachrowi, of the military headquarters' general information department, said on Friday.
"The principle is that all our forces in Aceh are basically continuing their duty under the security operation. But they also have to accord a large portion of their time for the humanitarian relief efforts.
"We continue to launch raids into suspected GAM (Free Aceh Movement) areas and our vigilance remains high."
Nachrowi's comments come despite Indonesian military chief General Endriartono Sutarto calling on Monday for an unprecedented temporary ceasefire with the separatists to shift focus on rebuilding the remote province.
Much of the western coast of Aceh, including the capital of Banda Aceh, was demolished in Sunday's massive tsunami that was triggered by a 9.0-magnitude earthquake in the ocean 150km from the province.
The Indonesian death toll from the tsunami is nearly 80,000 people, with most of the fatalities in Aceh, and the government expects the figure to head towards 100,000 as rescue workers reach remote towns and villages.
The inability to quickly rebuild infrastructure in Aceh is being partly attributed to the decades-old insurgency that has claimed the lives of thousands of people and has allegedly led to less development in the province.
Sunday's tsunami had measured
9.0 on the Richter scale
The Free Aceh Movement has been fighting for independence since 1976, and the government stepped up its military suppression efforts with a massive operation that began in May 2003.
Amid the apparent calls for a ceasefire, Indonesian President Susilo Bambang Yudhoyono urged GAM separatists on Thursday to lay down their weapons and join efforts to rebuild Aceh.
Unilateral ceasefireThe exiled Free Aceh Movement leadership announced on Tuesday that it had imposed its own unilateral ceasefire, but said there had been no evidence of the army having laid down its arms.
"We declared a unilateral ceasefire, but some of our people have been killed in ambushes," GAM spokesman Bakhtir Abdullah said.
"At this crucial time, there is a natural catastrophe and yet the military troops are still hunting GAM people"
Free Aceh Movement spokesman
Meanwhile, it emerged on Friday that five senior GAM leaders jailed last year for between 12 and 15 years had survived the floods that killed hundreds of their former inmates because they were recently switched to other prisons.
The leaders had begun serving their sentences in Banda Aceh's main prison, which became a death trap for prisoners when the torrents of water and mud swept through.
But four of the men - Amni bin Ahmad Marzuki, Nashiruddin bin Syahbuddin, Muhammad Usman and T Kamaruzzaman - were moved to a jail on Java in August as part of authorities' efforts to break communication among GAM prisoners.
The fifth, Sofyan Ibrahim Tiba, was transferred to Java about a month later.
Indonesia to host summit
Meanwhile, Indonesian Foreign Minister Hassan Wirayuda has announced that his country would host a major summit of global leaders to discuss tsunami devastation across Asia.
He said the conference, to be held in Jakarta on 6 January, will gather 23 heads of state, and United Nations Secretary General Kofi Annan.
Heads of state from India and Sri Lanka, which have both suffered massive casualties and damage, were expected to attend the summit as well as all 10 members of the Association of Southeast Asian Nations (Asean).
Representatives from the United Nations, the World Bank, the World Health Organisation, Asian Development Bank and European Union are also on the guest list.
Wirayuda said the meeting, chaired by Susilo, would "forge a joint commitment to encourage concrete action" for rehabilitating and reconstructing areas hit by the disaster.