Punongbayan received two presidential awards in 1992 and 1996, the Pagasa Award for Public Service in 1994, the Unit Award for Excellence of Service granted by the United States Department of the Interior in 1991, and the United Nations Sasakawa Award for Disaster Reduction in 2001.
In April 2003 he was awarded the Sergey Soloviev Medal of 2003 by the European Geophysical Society for his exceptional research and assessment of natural hazards. He had been only the fifth scientist to receive this prestigious award.
Established by the Interdisciplinary Working Group on Natural Hazards in recognition of seismology and tsunami research expert Sergey Soloviev's achievements, the medal is given to scientists who have made special contributions to the proper assessment and mitigation of hazards for the protection of human life and socioeconomic systems. Soloviev gained worldwide recognition as an authority in these fields and was a courageous advocate of the principles of international cooperation.
At the time of his death, he was serving as a member of the Philippine National Red Cross Board of Governors. Shortly after noon on April 28, 2005, Punongbayan and eight others died in a helicopter crash at Gabaldon, Nueva Ecija.
The passengers in the Philippine Air Force (PAF) Huey chopper No. 324 were him, four staff members of the Philippine Institute of Volcanology and Seismology (Phivolcs) and four Air Force crew members. They were on a mission to assess the area as part of the disaster preparedness operations program of the government and were also looking for possible resettlement for people displaced by flash floods and landslides.
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