Ambassador Burhan Muhammad sustained injuries when a Pakistan Army helicopter carrying him and others crashed in Naltar Valley in the Gilgit-Baltistan region on May 8, Dawn online reported citing Indonesian foreign minister Retno Marsu.
Ambassadors of Philippines and Norway and wives of the Malaysian and Indonesian ambassadors were killed in the same crash.
Two pilots and a crew member were also killed in the crash. The pilots were identified as Major Altamish and Major Faisal.
"Indonesia's foreign ministry has just lost one of its best diplomats, Ambassador Burhan Muhammad, who passed away at 00:50 on May 19 local time in Singapore," foreign minister Retno Marsudi said.
Prime Minister Nawaz Sharif expressed deep grief and sorrow over Burhan's death.
It was Pakistan's worst air crash since 2012, when a Boeing 737 passenger plane went down in Islamabad, killing 130 people.