Karzai has been the subject of growing criticism for his inability to halt the air raids.
Malik Hazrat, a protest leader, warned: "If the foreign troops do not put an end to their operations, we will launch jihad."
Karzai has also deplored the "civilian deaths" and demanded better co-ordination with the US army.
He warned that the deadly air raids were "strengthening the terrorists" and also weakening Afghan sovereignty.
A spokesman for the US military said it intended to investigate the incident.