Karzai's comments come as US-led forces prepare to launch a major offensive in Helmand province in southern Afghanistan.
Thousands of Nato and Afghan troops are converging for the operation, expected to start soon, aimed at capturing the town of Marjah.
General Stanley McChrystal, the commander of US and Nato forces in Afghanistan, said the offensive is intended to clear Taliban fighters from their southern stronghold.
"What we are looking to hear for this is to send a strong signal to the Afghan people, that the Afghan government is expanding its security control," he said.
"And so for an individual who lives for example in Marjah who right now lives under Taliban control with narco-traffickers there, they don't have a lot of choices so we're trying to create a situation where we communicate to them that when the government re-establishes security they'll have choices."
According to commanders, the offensive is set to be the largest assault against Taliban fighters since the war began in 2001 and comes just two months after Barack Obama, the US president, said he would send an additional 30,00 US troops to Afghanistan.
The Marjah plain, located in the central Helmand River valley is home to around 80,000 people and said by military officials to be the last bastion of Taliban control.
On Sunday, minivans were piled high with mattresses and clothing lined up at checkpoints as local residents prepared to leave the area ahead of the offensive.
The International Committee of the Red Cross (ICRC) said there was no way to count the number of people who have left Marjah because many have moved in with relatives or rented houses in nearby towns instead of registering for emergency relief.
Bijan Farnoudi, an ICRC spokesman, said the organisation was poised to react quickly if a refugee crisis arises.
Ghulam Farooq Noorzai, the head of the provincial refugee department, estimated that 90 to 100 families had already left the Marjah area because of concerns about the military operation.
He also said that refugee officials held an emergency meeting last week and decided to stockpile food and erect tents on a school compound in the nearby provincial capital of Lashkar Gah to accommodate any influx