Passos Coelho, speaking yesterday before parliament, acknowledged oversights but said he had dealt with the issues revealed in press reports in late February.
"I can guarantee to the entire country that I have regularised my situation," he said. "I have not obtained favours from the state or social security office."
Passos Coelho, Prime Minister since 2011, was twice interrupted by protesters in the gallery who yelled for him to resign before they were escorted away.
Confronted over the issue by a journalist in 2012, he went to the administration and was told of a debt of 2,880 euros (USD 3,038), with interest of 1,034 euros.
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Further press reports said the Prime Minister had also faced five tax adjustments between 2003 and 2007 that led to the payment of nearly 6,000 euros in penalties.
The tax authorities and social security office have confirmed that the prime minister paid his debts.
An online petition started on March 6 demanding his resignation however had been signed by more than 18,600 people as of yesterday, far more than the 4,000 signatures needed to force a parliamentary debate.