He conveyed his concerns to Egyptian Foreign Minister Nabil Fahmy during a telephonic call, the State Department said in a statement.
"Kerry expressed concern about the interim Egyptian government's December 25 terrorist designation of the Muslim Brotherhood, and recent detentions and arrests," it said.
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It said the two leaders agreed there can be no place for violence in Egypt and that the Egyptian people deserve peace.
Egypt's military-backed interim government declared the Brotherhood, to which ousted president Mohammed Morsi belongs, a "terrorist" group, blaming it for a suicide bomb attack on a police station that killed 16 people.
The Brotherhood has denied having a hand in the bombing, claimed by the al-Qaeda inspired group Ansar Beit al-Makdis.
The condemnation of the Muslim Brotherhood - considered the largest and best-organised political force in Egypt - came weeks ahead of a referendum on a new constitution that is described as a major step toward restoring democracy since the military removed President Morsi in July.
During the call, Kerry underscored the need for an inclusive political process across the political spectrum that respects the fundamental human rights of all Egyptians in order to achieve political stability and democratic change.
Kerry and Fahmy also discussed the issue of NGOs in Egypt, including the June 2013 verdict in the trial against NGO representatives. He also raised the need to redress the verdicts, the statement added.
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