A statement said that remarks by Kerry "threaten to cause the failure of the Geneva conference, are a flagrant violation of Syrian affairs and an aggression against the Syrian people's right to decide their future".
Kerry, who has been pressing for a peace conference about Syria in Geneva, said in Cairo that Washington and its allies may differ over "tactics" on the conflict, but they shared the goal of a handover of power.
"If the United States is sincere in its cooperation with Russia, Kerry must understand that only the Syrian people have the right to choose their political future, without foreign intervention," the ministry said.
"The success of (the proposed peace conference), Geneva II, depends solely on the Syrians' willingness to reach an agreement amongst each other, to put an end to violence and terrorism, and to reach a political solution," it added.
President Bashar Assad's government has brushed aside calls for his removal from power, branding peaceful opponents and armed rebels alike as "terrorists".
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