Defiant student supporters of the Brotherhood protested in Cairo last night, clashing with opponents of deposed Islamist president Mohamed Morsi in a flare up that left one person dead, the interior ministry said.
A ministry statement added that seven Brotherhood supporters had been arrested after police intervened with tear gas.
The Islamists vowed to continue their protests, despite the ferocious crackdown on their movement.
"Let's begin with full force and peacefulness a new wave of majestic anti-coup action," said the Brotherhood-led Anti Coup Alliance in a statement.
State Department spokeswoman Jen Psaki said Kerry had also "expressed concern" about the Brotherhood's designation as a terrorist group, in a phone call with his Egyptian counterpart Nabil Fahmy.
The intensified crackdown on the Brotherhood, which prevailed in a series of polls held after the 2011 overthrow of Hosni Mubarak, came after the military-installed government blamed it for a suicide car bombing of police headquarters on Tuesday that was claimed by a jihadist group.
The explosion yesterday shattered the windows of a red and black bus as it passed near a busy intersection in the capital's Nasr City neighbourhood.
Construction worker Mahmud Abd al-Al described scenes of panic after the attack, saying the victims were "covered in blood" and that one man lost a leg.
The attack was "meant to terrorise people before the referendum," interior ministry spokesman Hany Abdel Latif told AFP.
The interim government has billed the referendum next month on a new constitution as the first step in a democratic transition ahead of parliamentary and presidential elections.
It could mean death sentences for Brotherhood leaders and five years imprisonment for participants in its protests, the interior ministry's Abdel Latif told state television.
The move caps a dramatic fall for the Brotherhood since Morsi was overthrown on July 3 amid massive protests demanding the Islamist's resignation.
The Brotherhood had since Morsi's overthrow been organising almost daily protests, despite the fact that more than 1,000 people, mainly Islamists, have been killed in street clashes in recent months and thousands more arrested, including the Brotherhood's top leadership.
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