The votes of 8,494 polling stations, out of a total of 26,000, will be recounted, TOLO News reported citing the head of the IEC secretariat, Habib-Ur-Rahman Nang, as saying.
The pressure on the Commission has increased in the last few weeks with reports of fraud and the technical issues.
With 15 candidates, during the last few weeks, the counting has been interrupted due to allegations and obstacles by the team of major aspirants, including President Ashraf Ghani and his Chief Executive Abdullah Abdullah.
Meanwhile, Abdullah made his stance clear on the vote recounting process when he addressed a gathering of his supporters in Kabul on Sunday.
"Over the past forty-five days, the 2,400 ballot boxes were under the control of those who have plotted the whispered fraud, and anything can be found inside the boxes," Abdullah said.
According to Article 19 of the Election Law, only biometric registered votes should be recounted in case there are differences about them, TOLO News said.
"The non-biometric votes, as well as the votes that have been used on the election date, will be recounted. These votes must not be counted under any circumstances," presidential candidate Faramarz Tamanna said.
Besides Abdullah, the Council of Presidential Candidates - which includes up to 10 out of 18 presidential runners - also boycotted the vote recounting process on Sunday.
"Our stance is the same as the past. We wanted to boycott the elections; therefore, we boycott the results as well," said Shahab Hakimi, a presidential candidate and a member of the council.
But, a member of the State Builder campaign team led by President Ghani, said they respect the decision by the Election Commission.
"We support the Commission's decision to recount the votes," said Najib Danish, a spokesman for State Builder.
The presidential elections were held on September 28. According to IEC, the preliminary results will be announced on Thursday.
( With inputs from IANS )