"Obviously we are at a very critical moment for Afghanistan," Kerry said as he met the head of the UN assistance mission Jan Kubis in the heavily fortified US embassy in Kabul.
"The election legitimacy hangs in the balance. The future potential of the transition hangs in the balance, so we have a lot of work to do."
Kerry flew in on a hastily arranged mission, landing in the Afghan capital in the dead of night.
Later Friday he will meet poll rivals Abdullah Abdullah and Ashraf Ghani, who are locked in a bitter row over who won last month's run-off election to choose a successor to President Hamid Karzai.
The stakes could not be higher, as the next president will have to steer the war-torn country as international troops withdraw, leaving Afghan forces to fight a bloody, stubbornly resilient Taliban insurgency.
"Our hopes are that there is a road that can be found that will provide that capacity for the questions to be answered, for people's doubts to be satisfied and hopefully for a future to be defined," Kerry said.
But he warned that was not "an automatic at this point".
Kubis vowed the UN would do its utmost to help Afghanistan "finalise and complete the political transition... in a way that will strengthen the stability and unity of the country."
Preliminary results have put Ghani in the lead, but Abdullah, who has already once lost a presidential bid in controversial circumstances, has declared himself the true winner, saying massive fraud robbed him of victory.
The election stand-off has sparked fears that protests could spiral into ethnic violence - and even lead to a return of the fighting between warlords that ravaged Afghanistan during the 1992-1996 civil war.
Kerry was also to meet outgoing president Karzai, who has held the reins of power for 13 years.
"A perfect election in these conditions is neither possible nor really the objective," a senior US administration admitted.
The US was "going to push for the very best, most credible, most transparent and most broadly accepted outcome that we can under the circumstances," he said.
Ghani's campaign spokesman Abdul Ali Mohammadi said Kerry was "coming here to solve the election deadlock, and I think it is a positive step".
Abdullah's spokeswoman Lailuma Ahmadi also welcomed Kerry's visit, saying: "We welcome any move and efforts to separate clean votes from unclean votes or fraudulent votes".
Kerry will be pressing both candidates to accept a thorough audit, the US official said.
Auditors may look at districts with a very high turnout, or a perfectly round number of recorded votes, or where the number of women voters outnumbered men, "which in the Afghan context seems like an unlikely outcome".
Amid protests and political turmoil, the United States has warned both candidates that any attempted power grab will lead to an immediate cut in billions of dollars of annual aid.
After more than 13 years of war following the 2001 US invasion to oust the hardline Taliban regime, President Barack Obama has said all American forces will be withdrawn by the end of 2016.
The 30,000 US troops on the ground will be whittled down to 9,800 next year.
Eight million votes were cast in the run-off, and preliminary results showed Ghani took an estimated 56 percent, while Abdullah, the front-runner in the first round, got some 43 percent - a gap of around one million votes.
UN officials have said a full audit of the results could take up to two weeks, but some Afghan officials are pressing to stick by an election calendar that would see the new president inaugurated on August 2.
"We don't consider that an impossible goal," the US official said, but getting a credible outcome "was more important that sticking to a timeline".
The Obama administration is also desperately waiting for Afghan leaders to sign a bilateral pact governing the presence of US forces in the country beyond this year.
Karzai walked away from the deal, but both presidential candidates have said that they would sign it.
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@Afghan Maihan: I hope you are right. I hope I am wrong. My fear is that if small men like Karzai and Ghani make it the business of their lives to exclude Abdullah, we cannot expect the latter to take it lying down. Now, if Ghani is declared elected and takes office as duly elected president and if Abdullah proceeds to declare a parallel government, then it certainly makes for another phase in the Afghan civil war that we have been seeing since the ouster of Zahir Shah. There have been instances in Afghan history when there were two amirs in different parts of the country at the same time. That amounted to partition, whether on ethnic or any other grounds. Better rulers arose and re-unified the country. It remains to be seen if the present electoral tussle is resolved in a sensible way, say, by ordering re-polling under UN auspices and supervision. But as I said, Karzai and Ghani are small men. They are neither large hearted nor democrats. V. C. Bhutani, Edinburgh, 12 Jul 2014, 0820 GMT
@ Mr. Bhutani
With all due respect, Afghanistan is not going to be partitioned along ethnic lines and the prospect of warlords battling it out are slim. The whole thing is staged to dramatize the democratic process and salvage some legitimacy for the elections. John Kerry is in Kabul to save the day and do damage control.
@V. C. Bhutani: You have done quite a bit of writing to certify that there are too many factors of uncertainty! Also your thesis that the two situations in Afghanistan and Iraq were qualitatively different, is a diversion. The American forces went into Afghanistan and Iraq and others to destabilise the countries and the region, and this is how they are today completely destabilsed. John Kerry is the great destabiliser foreign secretary in the 21st century. This old vietnam veteran has not learnt that pointing fingers at others is rude!.
Rex Minor
The two situations in Afghanistan 2001 and Iraq 2003 were qualitatively different. But USA intervened in both. In the case of Iraq, no one had launched an attack on US interests anywhere. It was Americans’ visceral antipathy to Saddam Hussein that impelled Bush to imagine WMDs in Iraq: this was shown in due time to be a stark lie, not to use strong words. Even then US troops remained in Iraq a long time and when they left they gave the people of Iraq a gift of instability and non-government. US action in Iraq was designedly intended for regime change and for the elimination of Saddam Hussein. Having achieved that objective, USA achieved nothing else. Besides, Americans had not even the shadow of an idea what to put in place of Saddam Hussein’s government. With all his faults and failings, Saddam Hussein had kept Shias, Sunnis, and Kurds together in one country and he was not making WMDs. US war in Iraq was wholly unnecessary and unjustified. The people of Iraq have been suffering to this day, with no one big enough to lead the country. In Afghanistan, the case was different. The Afghan Taliban’s guests Al Qaeda had given egregious provocation to USA with 9/11. This brought USA directly in opposition to Al Qaeda and their hosts in Afghanistan. It is a moot question whether Obama would have been reticent about using troops on ground if he had been president in 2001. Having inherited a war, Obama prosecuted that war effectively but achieved none of the objectives with which Bush had started. US-led Allies brought Karzai to power with unconcealed support to him. The Allies erred and almost interfered in the Afghan elections in 2004 and 2009 when they declared their support and preference for Karzai: surely, Abdullah would not have grown fonder of the Americans for their pains. The Allies just did not know when to keep off. Their action amounted to interference in the Afghan electoral process. We have not heard now that anyone on USA’s behalf expressed US preference for either Abdullah or Ghani, but this time round Karzai made up for the restraint of the US. He worked overtime for and in behalf of Ghani and did his damnedest to scuttle Abdullah’s chances. Everybody is saying that some electoral fraud was expected but not on the scale that we see now. If the ballots are not properly audited now, there is hardly doubt that Ghani will be declared winner and Abdullah shall form a parallel government. If USA is not rash and extravagant about intervention now, then the Abdullah–Ghani rivalry shall play out, perhaps with some kind of a partition, possibly on ethnic lines. Things do not augur well for the Afghan people. Much will depend on whether USA shall leave them alone – and whether Pakistan shall leave them alone. As it is, Pakistan itself is unstable and confused in its attitude to its own Taliban and the Haqqani network. The current Pakistan army operations in North Waziristan are another source of instability in Afghanistan, especially in the Afghanistan–Pakistan borderlands. At the moment, the struggle between Afghan government and Afghan Taliban is not a factor of stability either. Pakistan wants Afghanistan to grab Fazlullah but no one in Afghanistan has grateful memories of Pakistan’s role in the past. Besides, Pakistan’s own attitude towards its Taliban is ambivalent. There are too many factors of uncertainty. V. C. Bhutani, Edinburgh, 11 Jul 2014, 1600 GMT
When you want to stick to democratic system with an option to control manually if the result do not match your desires then such failures happen whether it is Afghanistan, Egypt, Iraq, Syria or Algeria. US is a failure evetywhere.