Counting started in the northern oil-producing province of Kirkuk, a election commission source there said, and at least six other provinces were expected to follow suit in coming days.
Parliament ordered a full recount earlier in June after a government report concluded there were widespread violations.
That kicked off a politically fraught process as leaders of political blocs got embroiled in negotiations over the formation of the next government.
A panel of judges overseeing the recount later limited its scope, ruling that it would only cover suspect ballots flagged in formal complaints or official reports on fraud.
Overseas votes cast in Iran, Turkey, Britain, Lebanon, Jordan, the United States and Germany will also be recounted, the panel added.
Representatives from the United Nations and foreign embassies will attend the process, as will local and international observers.
One person was killed and 20 wounded in Kirkuk on Sunday when a suicide car bomb went off near a storage site housing ballot boxes. Police sources said the warehouse was not damaged.
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