Amanullah Aman, the head of the Independent Election Commission (IEC) in Kunduz province, was killed by two gunmen outside his home in Kunduz city as he left for work.
He was the first election official to be murdered since candidate nominations opened on Monday. All potential runners in the wide-open race to succeed President Hamid Karzai must declare themselves by October 6.
"Aman was shot dead in the morning in front of his house as he was leaving for his office," Kunduz provincial spokesman Enayatullah Khaliq told AFP.
Deputy police chief Ebadullah Talwar said that Aman was murdered after going grocery shopping and was not accompanied by any bodyguards. Talwar added that five arrests had already been made, but gave no further details.
The Taliban, who often target government officials, released a brief statement on their website claiming responsibility for the attack.
Last month Taliban leader Mullah Omar called the election a "waste of time", but has so far stopped short of threatening an increase in attacks targeting preparations for the vote on April 5.
Kunduz, which borders Tajikistan, is in the more peaceful north of Afghanistan, but it is still a hotbed of Islamist insurgent activity.
The province is also a major route for drug trafficking and has a volatile mix of rival ethnic groups and armed militia.
A successful presidential election next year is widely seen as the key test of international military and aid efforts since the fall of the Taliban in 2001.
"A good election this time will be good for my good reputation," he said.
"I will be involved until the candidates are registered... And I will only get involved again on polling day when I will cast my vote for my favourite candidate.
"I will remain neutral in all election deals, but will be providing security and will stop foreigners meddling in it."
Karzai has said former warlord Abdul Rasul Sayyaf, 2009 runner-up Abdullah Abdullah and former finance minister Ashraf Ghani were possible candidates.
