The ministry said in a statement that the European Parliament decision was based on "misinformation which reflects lack of awareness of the reality of the situation in Egypt."
The ministry said the European Parliament approach "does not serve the support of the bilateral relations between Egypt and the European Union."
"The decision violates the simplest democratic principles of the separation of authorities in tackling the matters in subjective way," the statement said.
Earlier Tuesday, the European Parliament issued a decision calling on Egypt to release all "political detainees", including members of the Muslim Brotherhood, the group from which ousted President Mohamed Morsi hails.
The decision called also for "putting an end to all violent activities against the opposition politicians, demonstrators, journalists, bloggers, students, women right activists, civil community representatives and minorities."
It also called for the release of 167 detained lawmakers who were elected in 2011.
Egypt has been dogged by instability when the military unseated Morsi, the country's first freely elected president, in mid-2013 following massive protests against his administration.
Egyptian authorities have launched a harsh crackdown on Morsi supporters, detaining thousands and killed hundreds.
While rights organizations talk about the presence of political prisoners in Egyptian jails, the military-backed authorities say those in prison are involved in criminal offences.