Karzai's request comes in the wake of a deadly gun battle between American and Afghan forces and Taliban insurgents in Kunar province earlier this month.
Karzai's spokesman Aimal Faizi told The Guardian on Friday the joint CIA-NDS units in Kunar were not under the control of Kabul, but answered to agency officials in Afghanistan.
"Some of them are said to be working with the NDS, but they are not armed by the NDS, not paid by the NDS, and not sent to operations by the NDS. Sometimes they only inform the NDS minutes before the operation," Faizi said of the paramilitary units.
"They are conducting operations without informing local authorities and when something goes wrong it is called a joint operation," he added.
As a result, Faizi said Karzai would begin reining in these joint commando units, limiting their ability to conduct operations in some of the most restive provinces in Afghanistan.
"The use of these parallel structures run by the CIA and U.S. special forces is an issue of concern for the Afghan people and the Afghan government," he said.
The Kunar attack ended with the deaths of 10 Afghan children, who were killed when NATO warplanes carried out an airstrike against a senior Taliban commander during the battle.
An American adviser to Afghan intelligence was also killed during the attack in Kunar.
The children, who were related to the Taliban commander, were in the house when NATO fighters took out the building.
U.S. and Afghan forces were taking heavy fire from the building during the attack before the airstrike was called, The Associated Press reported at the time of the strike.
"I don't think that they knew that all these children and women were in the house because they were under attack from the house and they were shooting at the house," Gul Pasha, a tribal elder in Kunar province, told the AP.
The CIA declined to comment on Friday on whether the U.S. adviser killed in the gun battle was an agency official.
In February, Karzai ordered U.S. special forces to leave Wardak, alleging American troops had committed torture and abducted civilians during their time in the province.
Karzai's announcement on Friday is another example of an increasing trend among Afghan leaders at the national and local level of playing to the growing anti-American sentiment within the country.
Sensing the end is near, local and national leaders are doing all they can to solidify their power bases across Afghanistan.
That pressure, he added, could force Afghan leaders -- particularly at the provincial and district level -- to forge alliances with the Taliban rather than the central government, to fill the power vacuum left after 2014.