Mr Doherty, 67, was found dead at his home at The Rock, Churchill last weekend.
Initial reports suggested he had died of natural causes.
Forensics officers have been carrying out investigations at the home all week.
Yesterday State Pathologist Marie Cassidy arrived at the scene and carried out a full examination of the area.
Inspector Eugene McGovern from Milford Garda station has confirmed that Mr Doherty suffered a “traumatic death” and was found on the bathroom floor of his home at Drumacanoo.
As a result of that investigation a statement from Gardai said: “Gardai in Millford are investigating all of the circumstances surrounding the death of a man in Churchill, Co Donegal on the 17th of June 2012.
“At approximately 1.50am on the 17th of June 2012 Gadrai and emergency services were called to a house at Drumacnoo near the village of Churchill where the body of 67 year old Seamus Doherty was discovered. He was pronounced dead at the scene and removed to Letterkenny Hospital.
“Following a post-mortem examination carried out by the State Pathologist Prof.Marie Cassidy on the 19th June the it was established that Mr Doherty had died in suspicious circumstances.
“An incident room has been set up at Letterkenny Garda Station and Gardai have begun a murder investigation.
“The scene remains preserved pending a full forensic and technical examination.
“Anyone with information is asked to contact Letterkenny Garda Station 074 9167100, or the Garda Confidential Line 1800 666 111.”
Locals in the Churchill area are shocked at the developments in the death.
Mr Doherty was well-known in the area.
He appeared before the local courts on a number of occasions for being drunk and disorderly.
He was also ordered to attend the psychiatric services by Judge Paul Kelly last March when he was found guilty of assaulting the local priest.