Meanwhile, the US State Department warned citizens not to travel to Egypt and called on those already there to leave.
Obama’s remarks sparked a defiant response from Egypt’s president early on Friday, saying that “statements not based on facts may encourage violent armed groups.”
“The presidency appreciates US concern for developments in Egypt, but it wished it could have clarified matters,” said the statement carried by the official MENA news agency.
Governments in several European capitals summoned Egyptian envoys to voice their concern.
Turkey’s Prime Minister Recep Tayyip Erdogan, a Morsi supporter, described the crackdown as a “massacre” and Ankara later recalled its ambassador to Cairo.
And UN rights chief Navi Pillay called for “an independent, impartial, effective and credible investigation of the conduct of the security forces.”
“The number of people killed or injured, even according to the government’s figures, point to an excessive, even extreme use of force against demonstrators,” she said.
Morsi supporters had called for Cairo marches on Thursday but that call was not heeded, while small protests were staged in coastal Alexandria and southern Beni Sueif.
Meanwhile, attacks against churches and Christian properties that began on Wednesday continued for a second day, with activists saying at least 25 churches had been targeted.
As relatives sought to identify their dead, Brotherhood spokesman Haddad insisted protesters would “remain strong, defiant and resolved.”
“We will push forward until we bring down this military coup,” he tweeted.
In Cairo, at the Al-Iman mosque, dozens of corpses of protesters clad in white shrouds were lined up before grieving relatives.
At the two protest sites where Morsi loyalists had camped since his July 3 ouster, trucks cleared charred debris.
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