Jaap de Hoop Scheffer said: "There was no point in negotiating with the Taliban, since they were only interested in harming Afghanistan and undermining efforts to build democracy."
"I can't imagine that Nato would negotiate with people who kill children or teachers in school"
Jaap de Hoop Scheffer, Nato's secretary-general
Interviewed on German television, Scheffer was asked if he believed that there could be peace talks with the Taliban.
"I don't think so, not when you're dealing with people who have the goal of destroying the reconstruction and democracy," he said from Berlin where he was attending a conference on European defence policy.
"You can't negotiate with them. I can't imagine that Nato would negotiate with people who kill children or teachers in school."
Karzai has previously offered amnesty to those Taliban he and others regarded as "moderate", but on Monday he made no such distinctions.
No senior Taliban commander or leader has surrendered or joined the government as part of past efforts to bring them into the mainstream and senior leaders have ridiculed such calls as a sign of weakness.
More than 4,000 people, including about 170 foreign soldiers, have died in fighting in 2006, which saw a dramatic jump in suicide bombings. Taliban commanders have also given warning of a large summer offensive this year.
Nato has 32,000 troops stationed in Afghanistan.
Taliban forces have vowed to drive out foreign troops and overthrow Karzai and his government.