If genuine, the letter marks a turnaround from a directive issued by the Taliban a year ago when Omar urged fighters to avoid harming civilians even if they had been captured.
"We believe this guidance provides important insights into recent events as you may be aware the Taliban are causing an alarmingly high number of civilian causalities, and they have also begun attacking those who have chosen to serve the people of Afghanistan as public servants," Brigadier-General Josef Blotz, a spokesman of the Nato-led International Security Assistance Force (Isaf) said at a news conference in Kabul on Sunday.
'100 per cent sure'
Blotz said he was "100 per cent sure" the letter was from the Taliban leader, although he could not reveal how it had been verified in order to protect Nato's sources.
The Taliban could not be immediately reached for comment.
Violence is at its worst in Afghanistan since US-led forces overthrew the Taliban in late 2001 for refusing to give up al-Qaeda members following the September 11 attacks in the United States.
Omar, seen as the founder of the Taliban movement that emerged during the civil war of the early 1990s, has not been seen in public for years. He is believed to be in Pakistan.
While other leaders are believed to be more involved in the day-to-day command of the insurgency in Afghanistan, Omar is still considered the spiritual head of the movement.