"It will be fair," Grant Kippen, the head of the ECC, said.
"We've got these international experts who have been doing this and who have advised that this is a good approach."
The 313 ballot boxes were randomly selected in front of candidate agents and observers, Nellika Little, a spokeswoman for the ECC, said.
The selected ballot boxes could be retrieved from the provinces as soon as Saturday, according to Zekria Barakzai, the deputy chief electoral officer of the Afghan election commission.
Officials suggested that the process would take about two weeks.
The IEC has said that it wants to make the process as quick as possible in case a second run-off is needed between the two leading candidates.
If no candidate wins at least 50 per cent of the official results the two candidates with the highest number of votes will go into the runoff.
The IEC announced final preliminary results for the election last week giving incumbent Hamid Karzai 54.6 per cent and Abdullah Abdullah, a former foreign minister, 27.8 per cent of the vote.
The results will not be confirmed until all cases of fraud are investigated.
There have been concerns that further delays would make it virtually impossible to hold a run-off before the harsh Afghan winter, which would likely prevent election materials being delivered to many polling stations.