Baghdad province accounts for about a fifth of parliament's 325 seats. Al-Maliki had challenged results in four other provinces as well, but had those requests denied.
The recount was being carried out inside the green zone under the supervision of observers from the UN and the European Union.
Iraq's March 7 parliamentary poll produced no clear winner, with Allawi's Iraqiya coalition winning the highest number of seats, 91, and al-Maliki's State of Law bloc coming a close second, with 89 seats.
A political bloc needs 163 seats in parliament in order to form a government.
However, coalition-building talks between the major blocs and smaller parties in order to achieve that number appear to have stalled.