He met his Israeli counterpart Avigdor Lieberman in Brussels last week at a meeting of EU foreign ministers. Mr Martin later travelled to Gaza.
In a statement he said: “I fully understand and share the deep concerns which many people in Ireland feel in regard to Israel’s policies on a number of issues.
“However, it is a basic principle of relations between states that we treat each other’s diplomatic representatives with civility and respect, regardless of any policy differences. To do otherwise would seriously undermine the ability of states to conduct international relations.”
He said citizens moved to protest against a government’s policies should do so “peacefully and in a way that respects the diplomatic status and personal dignity of the Ambassador”.