According to the interior ministry, the troops were deployed by Olexander Kikhtenko, the commander of the ministry's military branch.
Kikhtenko backs Yushchenko and no longer recognises the authority of Vassyl Tsushko, the minister of interior and a supporter of Viktor Yanukovich, the prime minister.
Tsushko appealed for calm, asking "politicians to be more restrained".
Tens of thousands of troops serve in the interior ministry's military branch as well as police and paramilitary units.
Meanwhile, crisis talks between Ukraine's feuding president and prime minister resumed on Saturday, Laryssa Mudrak, a spokeswoman for the presidency said.
A power struggle between Yushchenko and Yanukovych has escalated in the last two days as both sides claim the loyalty of rival security forces.
Rival supporters have repeatedly protested during the political standoff [AFP]
The two held talks in an attempt to defuse an escalating political crisis and settle a battle for control of interior ministry forces.
Yushchenko and Yanukovich had initially met on Friday after the president took control of the troops in a move the prime minister said was "anti-constitutional".
Yushchenko issued a decree placing the troops under his command hours after riot police loyal to the prime minister took over the prosecutor-general's office in Kiev.
The presidential decree concerned 32,000 troops largely responsible for maintaining public order and not the army, which is controlled by one of Yushchenko's few allies in the cabinet.
He ordered the interior ministry troops to protect key sites.
|The two Viktors: No smiles |
for the camera [AFP]
Yanukovich said the president’s move was dangerous and unconstitutional.
"Taking such decisions without consulting the government is inadmissible. I think this seriously aggravates the situation," he told an extraordinary cabinet meeting.
"What does all this mean? This means that the 'use of force scenario', which we have been discussing constantly, has begun."
Yushchenko responded by saying he held "little optimism" any new talks with Yanukovich and his ruling parliamentary coalition would help resolve the situation.
The two Viktors are long standing political rivals dating back to the country’s "Orange Revolution" in 2005 when mass protests led to a re-run of a presidential vote originally won by Yanukovich but annulled because of fraud allegations.
Yushchenko won the re-run but in last year's parliamentary elections, Yanukovich's party won the largest share of seats.