"The invaders and their allies should understand that inking strategic agreement would be accompanied by dire consequences," Mullah Mohammad Omar said in a message posted on the militant group's website.
He also warned Afghans would not accept the agreement even if it was approved by "a fake Loya Jirga," a grand council composed of tribal elders, Indo-Asian News Service reported Monday.
If finalized, the agreement would allow the United States to keep a limited number of troops in Afghanistan past the 2014 date at which the NATO-led coalition will withdraw from the country.
Some nine U.S. bases would reportedly remain in the country.
Omar warned "no foreign military base is acceptable," saying attacks on any bases would be intensified.
Omar also called on Afghans to boycott the April 2014 presidential elections.