McChrystal, a former commander of special forces in Iraq, is due to take command of the 56,000 US troops and 33,000 others from Nato countries shortly, replacing General David McKiernan, who was effectively dismissed last month.
"One of the things we will do is review all of our rules of engagement and all the instructions to our units, with the emphasis that we are fighting for the population and that involves protecting them both from the enemy and from unintended consequences of our operation," McChrystal said.
"We know that while an operation may be conducted for the right reasons, if it has negative effects it can have a negative outcome for everyone."
David Chater, reporting for Al Jazeera from Kabul, the Afghan capital, said that the planned troop increase in the country would likely lead to more deaths and consequently make McChrystal's task more difficult.
"It's bound to be the case that they [the extra troops] will go after the Taliban in their safe-havens, in their sanctuaries," he said.
"That means, with more boots on the ground, you're going to get many more casualties ... and the civilian casualties are already totally unacceptable here."
An air raid last month in western Afghanistan killed a large number of civilians.
The US military acknowledged 20 to 35 deaths, but the Afghan government insisted that the figure was 140.
In another incident, the US military said on Thursday that it had launched an investigation into allegations of civilian deaths from an air raid in the western Ghor province.
McChrystal hopes to limit the number of civilian casualties, saying in his TV interview that "the most important part is shielding the Afghan people".
"He has got a very clear idea [how to limit civilian casualties] - which is to get the troops out of the bases and into the villages, into the tribal areas," Chater said of McChrystal's plan.
"To try to develop a hearts-and-minds mission, give them some feeling of stability and increase the national intelligence network.
"They believe that will mean there won't be so many mistakes of American jet fighters bombing the wrong compounds and bombing women and children."
McChrystal's comments came a day after the commander of US forces in the Middle East and Central Asia said violence in Afghanistan had jumped to its highest levels since the fall of the Taliban in 2001.
"The past week was the highest level of security incidents in Afghanistan's history, at least that post-liberation history," General David Petraeus, the head of the US Central Command, told a forum in Washington DC on Thursday.
Petraeus said "there are some tough months ahead. Some of this [violence] will go up because we are going to go after their sanctuaries and their safe havens as we must".
Attacks soared by 59 per cent to 5,222 incidents from January to May, compared with 3,283 attacks in the first five months of 2008, according to US military officials and excerpts of a report by Nato's International Security Assistance Force (Isaf).
There were 1,450 attacks in May, according to Isaf, surpassing the 1,400-mark for only the second time since January 2007. The last time monthly attacks topped 1,400 was last August.