Mr Higgins said that Christian organisations, including the Catholic Church, were not asking questions about the EU's military agenda while, at the same time, it was telling people to "love their fellow man".
"I'm not looking for direction from the Catholic Church. It is puzzling that it wouldn't raise the issue of armaments.
"To have a major economic power bloc blatantly providing for more criminal wastage of resources on weapons of massive destruction in the face of massive poverty and destitution on our globe should surely be a cause for strenuous objection," he said.
Mr Higgins joined other anti-war organisations yesterday, including the Peace and Neutrality Alliance, to promote a 'No' vote in the Lisbon referendum.
They argue that the EU armaments industry is given a formal place in the Lisbon Treaty.
The role of the European Defence Agency (EDA) is essentially to co-ordinate the armaments industry in the EU, making it an integral part of EU operations, they said.
Meanwhile, the Catholic Church last night refused to clarify its official position on the Lisbon Treaty.
An Irish Bishop's Conference statement issued on Monday night said that Catholics were free in conscience to vote 'Yes' or 'No' on October 2.
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