Boris Kondarko, who comes from the opposition Social Democrats, said that he was resigning “for personal reasons”, the party spokesperson, Petar Silegov, said.
However, Kondarko is yet to formally tender his resignation.
Silegov added that the opposition retains the right to propose another head of the commission, according to a deal with the government.
Kondarko’s personal reason for leaving the office leaves many observers unconvinced.
The resignation comes ahead of the March presidential election and after Kondarko found himself caught in public exchange of accusations between Prime Minister Nikola Gruevski and the opposition leader, Zoran Zaev.
The opposition accused the ruling VMRO DPMNE party of obstructing efforts to clean up the electoral roll ahead of the March presidential elections by using its majority on the commission.
The opposition said the centre-right government under Gruevski had an interest in concealing fictional or deceased voters on the electoral roll, which Social Democrats say are being used to tip election results in the government’s favour.
“Purification” of the electoral roll has been one of the key demands of the opposition in the past year.
Prime Minister Gruevski then accused Kondarko of being the one to block the work of the commission and urged “his boss”, opposition head Zaev, to order him to unclog its work.
Gruevski insisted that Kondarko had been blocking its work for six months, since the last local elections this March.
Kondarko called the accusations absurd.
“When the majority on the commission is appointed by the government it is absurd to claim that the president [of the commission] has the power to stall its work,” Kondarko said.
Earlier this week, replying to Gruevski, Zaev said the party was considering recalling Kondarko from the post as his presence there was pointless owing to the government’s blockade of the commission’s work.
The electoral roll has been a matter of controversy for some time.
The OSCE, which has monitored Macedonia’s past elections, describes it as unusually large for a country of just over 2 million people. The OSCE said it suspected the roll contained various fictional or deceased voters and urged officials to check the list in order to diminish suspicions of election fraud.
Despite claims by the Justice Ministry that the roll has been cleaned up several times, it has continued to grow.
The roll in 2008 contained 1,779,000 voters. In February 2010, after allegedly being cleaned up, it contained 1,792,000 voters and in March 2011, the Electoral Commission added some 43,000 more, bringing the total to 1,835,000.
Kondarko was appointed head of the commission in April 2011 after the government and the opposition hammered out a so-called gentlemen’s deal that the post should belong to the opposition and while the ruling parties should have the majority on the body.