Mr Howard said yesterday that East Timor - where Canberra is sending 1,300 soldiers to help quell a military rebellion - has a "significant governance problem".
"We consider this an interference in the internal affairs of East Timor and ... we disagree with this kind of statement by foreign countries," the Portuguese minister said.
Mr Howard has made it clear his government expects East Timor to enact political reforms in return for Australia sending troops to the fledgling nation.
"If things get out of control, and they clearly have, and outside help is needed, then those who provide the outside help are entitled to ask those who they are helping, 'Will you make sure that you run the country in future in a way that doesn't allow this to happen?'" Mr Howard said.
The Portuguese minister also warned of the dangers of civil war in his country's former colony, lamenting in particular strains between its president and prime minister.
Portugal is sending 120 troops to help end the violence in East Timor. After the end of four centuries of Portuguese rule, East Timor was invaded by Indonesia in 1975, but gained independence from Jakarta in 1999.