Another area commander said his men were "ready to attack" the warlord's forces at a signal from Karzai.
There was no immediate word of such orders from the president's office. The situation in troubled Paktia province and neighboring Khost region was believed to have been on the agenda of Monday's weekly meeting of Karzai's Cabinet.
The Pakistan-based independent Afghan Islamic Press (AIP) reported that a warning from Kabul was broadcast by state-run Kabul Radio late on Sunday.
"The state warns these criminal elements to stop their subversive activities, otherwise it would be forced to take action under the authority given to it by the Loya Jirga (grand assembly that elected Karzai as leader)," it said.
Bacha Khan Zadran's gunmen, who have allied themselves with the United States in its war against Taliban remnants and al Qaeda fugitives, have sought to assert control over parts of the region in defiance of governors appointed by Karzai's seven-month-old transitional government.
Zadran has been wanted by Karzai for ordering rocket attacks that killed 30 residents of Gardez, the capital of Paktia, in May.
The area is one of several flashpoints where local armed factions are vying for power in outlying areas of Afghanistan and is also one of the most active fronts in the U.S.-led war against al Qaeda and the Taliban.
"The situation is calm today," Mohammad Khan Gorbuz, a spokesman for Khost's governor, Hakim Taniwal, told The Associated Press by satellite telephone. "But we are seriously asking the central government to proceed with action against Bacha Khan."
He said Zadran's gunmen continued to man checkpoints along the roads, extorting money from travelers, and were coming and going in the town of Khost, the area's capital, which Gorbuz claimed otherwise was under Gov. Taniwal's control.
Reached by The AP late Sunday, a defiant Zadran said of Karzai, "If he wants to attack, I'm ready to defend." The warlord continued to assert his "right" to be regional leader of not only Paktia and Khost, but also the province of Paktika to the southwest.
In Paktia, where Zadran's forces control a stretch of the main road toward Khost, a local commander loyal to the national government said his men were ready for action.
"As soon as the central government organizes and gives the order, we are ready to attack," said Abdul Matin Husainkhil, commander in Paktia's Zormat district.
A statement Sunday by Karzai's office that named Zadran said the government "cannot tolerate these disturbances anymore and is giving serious warning to the enemies of peace and stability in the country."
After a U.S.-led military campaign brought down Afghanistan's Taliban government last December, Zadran was appointed governor of Paktia, about 75 miles south of Kabul, the Afghan capital. But local officials in the provincial capital of Gardez, backed by their own militia, refused to allow him to enter the city and take office.
Zadran withdrew after several days of fighting and the appointment was rescinded. He and his hundreds of fighters, armed with tanks and artillery, then set up their base in the neighboring Khost area.
There they fought other armed factions for power over an area that, among other things, generates customs revenues from goods imported by road from neighboring Pakistan.
Zadran has occupied the governor's house in Khost province and openly opposed Karzai's rule.
His Pashtun supporters staged protests there last week accusing Karzai, himself a Pashtun, of leaning towards the Tajik-dominated Northern Alliance and demanding his removal.
They have demanded the removal of men Karzai appointed as governors of the eastern Paktia and Khost provinces -- Raz Mohammad Dalili and Mohammad Hakim Taniwal.