Observers say the process - already heavily criticised by Western observers - has been rigged to secure the new parliament's loyalty before 30 October elections at which Akayev, 60, has vowed to stand down.
Among those standing in the second round is Akayev's daughter, Bermet, whose brother Aidar clinched a seat in the first round, fuelling claims that the previously somewhat independent parliament is being fashioned to protect the first family.
With several figures of questionable loyalty already disqualified in the first round, the authorities are putting the finishing touches to a race that leaves little for voters to decide, critics say.
Before Sunday's polls, an opposition candidate in the remote Naryn region was disqualified for starting his runoff campaign too early, in what observers said was probably the first in a series of such rulings leading up to polling day.
While there has been little sign of the Ukraine-style popular uprising that some opposition figures have hoped for, the government has not had things all its own way.
The first round was marked by angry exchanges between the government and US officials keen to show democratic gains in Central Asia to accompany Washington's basing of air force units in Kyrgyzstan and Uzbekistan.
Since then, government warnings against attempts to foment unrest have focused on southern Kyrgyzstan, a distinctive region bordering Uzbekistan that for centuries was part of the Silk Road trading route between Europe and Asia.
Opposition there has been sharpened by claims that Akayev has pandered to the Uzbek minority after Kyrgyz-Uzbek clashes in the Soviet Union's last months that left hundreds dead.
About 1.4 million citizens are
to vote in the elections
In recent days the south has seen a spate of unrest, including the occupation of the governor's office in the key region of Jalal-Abad by protesters who claimed the authorities had engineered wins by candidates of Uzbek origin.
Security forces used force on Saturday to break up a demonstration of 500 people in Ivanovka, a village in the Chui electoral district close to Bishkek, injuring numerous people and leading to the hospitalisation of one man, witnesses said.
The protesters were demonstrating against a regional court decision on Friday disqualifying a non-party candidate, Turatbek Andashev, from standing in Sunday's runoff election for allegedly buying votes.