A statement on the presidential Web site said his order for the troops to be under his command was necessary "to prevent using Interior Ministry troops in the interest of some political forces that cause a threat for Ukraine's national security."
On Thursday, the Interior Ministry, led by an ally of Yushchenko's arch-rival Prime Minister Viktor Yanukovych, sent police to surround the office of the prosecutor-general, whom Yushchenko had just fired.
The dismissal severely aggravated tensions that have been high since Yushchenko's April 2 order dissolving parliament and calling early elections. The parliament, where Yanukovych leads the majority coalition, has defied that order.
The dissolution order led to weeks of argument and competing demonstrations between backers of the president and of the premier, but no disorder broke out.
But Yushchenko's order on Friday, reflecting doubt on the loyalty of the substantial number of servicemen under the Interior Ministry's command, appeared to indicate that concern was rising over possible clashes.