Mr Lavrov said some victims had been killed at close range in a district controlled by rebels.
The UN condemned the killings, saying government artillery was involved. Russia is a close ally of Syria.
UN-Arab League envoy Kofi Annan has arrived in Damascus for talks on implementing his six-point peace plan.
He called on "every individual with a gun" to lay down their arms.
"I have come to Syria at a critical moment in this crisis," Mr Annan said shortly after his arrival.
"I am personally shocked and horrified by the tragic incident in Houla."
At a joint news conference with UK counterpart William Hague in Moscow, Mr Lavrov said that Russia was "deeply alarmed" by the massacre in Houla.
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