Afghanistan's second direct presidential election will be held on August 20, with Hamid Karzai, the incumbent president, a clear front-runner ahead of 38 challengers.
Earlier this month, US marines and British troops launched two major offensives in Helmand to secure areas previously held by Taliban fighters.
Holbrooke has been in Afghanistan since Thursday and has visited Helmand and Kandahar.
"You hold the best election you can under the circumstances ... it isn't going to be perfect"
US special envoy to Afghanistan and Pakistan
Before the Helmand operations, violence across Afghanistan had already reached its worst levels since the Taliban were removed from power in 2001.
Holbrooke, who visited the election commission data centre in Kabul, said "nobody's going to back down in the face of this intimidation", describing the difficulties faced by Afghans as "unprecedented".
"What do you want the Afghan people to do? To abandon the election because of some threats from a small minority of Taliban? Impossible. You hold the best election you can under the circumstances ... it isn't going to be perfect."
Zamary Bashari, a spokeman for the Afghan interior ministry, told Al Jazeera security forces would "do their best to provide security and pave the ground for the Afghan people to go and vote".
"We must not forget [that] the enemies of Afghanistan will always try to deter and dismantle the process of securing the election," Bashari said.
'Tired of war'
Sayed Jalal Karim, one of the presidential candidates, told Al Jazeera: "We should have elections. We should have the democratic process to go ahead. Afghan people are tired of war."
He said he had visited more than 12 provinces in Afghanistan and that he had had no problem going to the countryside.
|About 4,000 US marines are battling
pro-Taliban fighters in Helmand [AFP]
"We do face some security problems: for example, the government does not give us bulletproof cars, and I don't know the reason for that but we do believe that this is a challenge we have decided to take on," Karim said.
"The campaign has been going very well in north and the east ... I have held rallies and more than 10,000 people have attended my rallies.
"The people are ready for change and will participate in the elections."
Holbrooke said he was most concerned about women not being able to get access to polling stations.
"This election faces many complex challenges ... How we make sure women can vote, which requires women at polls as poll watchers, as people inspecting, and so on," he said.
Women have long been under-represented in politics and public life in conservative Afghanistan.
An International Crisis Group (ICG) report last month also raised fears that poor security and the failure to capitalise on gains made since the last election in 2004 meant widespread fraud was possible.