Now living in the Waikato and working as an electrical linesman, Anderson remembers wondering why he was leaving his family to go to another country he knew nothing about to protect people "I don't really know ... yeah, there were a lot of mixed thoughts on the day that I left."
During his time away Anderson got one leave break to come back to New Zealand.
Other than that he, like his colleagues, eagerly looked forward to letters and parcels from home, and a treasured satellite phonecall "every three or four months".
He found the separation from his son and family hard.
Jaynus lived with his mother, who had separated from Anderson before the peacekeeping mission, while his father was away.
Anderson, now 37, left the Army in 2003.
"It came down to what was more important, my career or my son."
There was no competition, he said.
Jaynus came to live with Anderson, visiting his mother Sofia regularly.
As for the East Timor tour of duty, Anderson described it as "life changing".
"It helped you appreciate home."
Jaynus, now 17, still lives with his father and is studying at a pre-military course with a view to following in his father's footsteps by joining the defence force.
He remembers feeling "pretty gutted" the day his father left for Indonesia.
"I missed him when he was gone."
Only now does Jaynus realise the sacrifice his father made in leaving the Defence Force.
"He loved the Army. He gave up heaps to be with me. I really appreciate that."