The move comes after Berkut riot police from the ministry -- which is loyal to Yushchenko's rival, Prime Minister Viktor Yanukovych -- occupied the office of Prosecutor-General Svyatoslav Piskun in an attempt to block his sacking on May 24 by the president.
Yushchenko issued the decree a day after he accused Interior Minister Vasyl Tsushko of breaking the law by ordering riot police to protect the Prosecutor-General's Office in Kyiv.
Tsushko had given the order after accusing Yushchenko of an "attempted coup" for firing Prosecutor-General Piskun.
The riot police, for the meantime, continue to occupy Piskun's office.
RFE/RL correspondent Tetyana Yarmoshchuk reports some 2,000 protesters divided between the Yushchenko and Yanukovych camps gathered today outside the Prosecutor-General's Office. Many were singing songs and urging a peaceful resolution of the standoff.
Approximately 40 Berkut troops wearking flak jackets and holding rubber truncheons were guarding the main entrance to the building. Piskun remained inside the building together with a group of lawmakers from the ruling coalition.
Opposition lawmakers and journalists were barred from entering the building.
A spokesman for the Interior Ministry told RFE/RL that the ministry rejected Yushchenko's decree.
In a defiant statement earlier today, Interior Minister Tsushko told lawmakers he did not abuse his powers in calling for the riot police to protect Piskun's office.
"It was said yesterday that I exceeded my authority," Tsushko said. "I didn't exceed anything. I gave my orders in full consciousness."
Defense Minister Anatoliy Hrytsenko, who is loyal to Yushchenko, warned security forces not to escalate the conflict.
The president and the prime minister have both sought to assure the country that there will be no use of force as the two sides look to resolve their political standoff.
In a nationally televised address on May 24, Yushchenko said the security services and armed forces will not be drawn into the dispute.
"There is one way out of the current situation. It is a political agreement," the president said. "People with arms will not help resolve this conflict. On the contrary, their involvement in this conflict would delay a political resolution. The manipulation of the work of the Prosecutor-General's Office is delaying a resolution of this issue."
Yanukovych, in his own televised statement the same day, affirmed that the country will not descend into anarchy.
"Let me assure you, my fellow countrymen, the government will allow no anarchy in Ukraine," Yanukovych said. "It will allow no civil war."
Piskun, however, isn't going to go quietly. Yushchenko justified the sacking by saying Piskun should not serve simultaneously as prosecutor-general and as a member of parliament. He said the current political stalemate is due in part to Piskun's dual roles.
Piskun, however, has called his sacking illegal and pledged to defy it.
"I wrote a request asking to resign as a member of parliament and sent it to the Verkhovna Rada within the term prescribed by the law," Piskun said on May 24. "You understand that this decree [to fire me] is absolutely illegitimate and even absurd, because on the 14th of -- well, everybody knows that I wrote this request, all staff members know that."
Yushchenko and Yanukovych have been locked in a power struggle since the president dissolved parliament in April and called for early elections.
Yushchenko has named Crimea's prosecutor-general, Viktor Shemchuk, as the country's acting prosecutor-general.
Yanukovych cut short a trip to Crimea and returned to Kyiv to convene an emergency cabinet meeting.
And Yushchenko has canceled a trip to meet with Central European leaders in the Czech Republic. He is currently in a meeting with security officials.
Yanukovych's allies are planning a rally for later today in downtown Kyiv.
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RFE/RL's Ukrainian Service asked people on the streets of Kyiv on April 11 whether the Constitutional Court will be able to determine the constitutionality of the president's decree dissolving parliament.
Oksana, a student from Lutsk:
"Their decision will at any rate be beneficial to one of the political forces."
Oleksandr, a high-school student:
"[The court] will be able to do it, but only if the judges agree upon it."
Alla Asilyevna, a pensioner:
"How can the Constitutional Court solve the problem if there is pressure on it from all sides?"
Ivan Yukhimovich, a pensioner:
"If [Prime Minister Viktor] Yanukovych and [President Viktor]Yushchenko find an agreement, everything will be resolved."
Yuliya, a worker:
"I doubt very much that the judges will agree on anything."