The Romanian foreign ministry described Voronin's comments as a "provocation".
"It is not acceptable that the communist power in Chisinau transfers responsibility for the Moldovan Republic's domestic problems onto Romania," it said in a statement.
Rodica Pricop, editor-in-chief of the Nine O'Clock newspaper in Romania, told Al Jazeera there was no truth in the allegations that Bucharest was behind the protests.
She said: "The Romanian authorities denied all the accusations made by president Voronin today.
"It is just a way to blame Romania or a foreign country for their own domestic problems. It seems like an absurd situation.
"Of course most of the people protesting in Moldova are youngsters and there are students who have relatives in Romania or are studying in Romania - they are pro-Romanian because obviously Romania and Moldova share the same in history, the same language, for thousands of years."
Moldova was part of Romania in the years that followed World War I, before being annexed by the Soviet Union in World War II.
It has shared a difficult relationship with Romania, which as a new European Union member has attempted to persuade Moldova to stay on a pro-Western path.
Relations between the two countries appear set to deteriorate further over the latest incidents.
Customs authorities said on Wednesday that Moldova had closed its border crossings with Romania, only allowing Moldovan citizens living in Romanian towns through.
"From 1000 (0700 GMT), customs authorities from the Moldovan Republic have restricted activity at all customs points with Romania ... allowing entry only to Moldovan citizens from localities near the border," it said.
Moldovan police are preparing for another day of anti-government protests in the wake of violent demonstrations in the capital.
|The protests were the worst disturbances Moldova has seen in recent years [AFP]
Voronin said on Wednesday that the authorities would use force to prevent a repeat of protests, which were aimed at his ruling Communist party.
The president said authorities had every right to stop the riots, the worst disturbances in recent years the country.
"I tried to not allow blood to flow in similar situations in 1989 and 1991," Voronin said, referring to his decision not to fire on protestors when he was interior minister in the last years of Soviet rule.
"But yesterday I was on the edge, as such a decision was needed. If this is repeated such measures could be taken. The authorities have every right to take them in line with the law."
The demonstrations by at least 10,000 mostly young people turned violent on Tuesday as people stormed and ransacked the parliamentary and presidential buildings.
Windows were smashed and furniture was removed from the buildings and subsequently set on fire.
Demonstrators are demanding a re-run of the vote, which international observers have declared to be free and fair.