A UN-backed election watchdog has declared invalid hundreds of thousands of votes for Afghanistan's president in the disputed August election, apparently stripping Hamid Karzai of outright victory and setting the stage for a second round.

After nearly two months of investigations, the Electoral Complaints Commission (ECC) – controlled by a majority of non-Afghans – found Karzai's total had fallen to 48.3%, according to an independent analysis. He needed 50% to clinch another term in office.

A separate election commission that backs the president will have to endorse the findings and call for a second-round vote to be held in the next few weeks.

"Now that we have the ECC orders, we expect the IEC [Independent Election Commission] to implement those orders with haste and move swiftly to issue the final certified results or the need for a runoff as required by Afghan electoral law," said Aleem Siddique, a UN spokesman in Kabul.

According to the independent analysis by the US-based Democracy International, Karzai's share of the vote fell from 55% to 48.3% after fraudulent votes identified by the EEC were stripped away. The figures confirmed views expressed anonymously by several foreign diplomats and election workers that Karzai's share of the vote had dropped to around 48%.

The president's closest rival, Abdullah Abdullah, gained from his preliminary tally of 28% to 31.6%.

A spokesman for the Karzai campaign, Moen Marastial, said they would accept only the results published by the Independent Election Commission, an Afghan-led organisation thought to be heavily partisan in favour of Karzai.

"Nothing has been officially announced so far. Only the ECC has said some votes should be disqualified," Marastial said.

He warned that the IEC could disagree the ECC's findings. "I don't know whether they will accept it or not. They have the right to work on the procedures and formulas of the investigations and after that they will decide whether they will accept or not, if it is according to international rules of investigation," he said.

In its published findings, the ECC stressed that the IEC was constitutionally bound to accept its orders. Marastial said Karzai may also refuse to accept the results if there was evidence of "interference in the fraud investigation". Karzai's supporters have several times suggested that the ECC is controlled by foreign interests.

Any refusal by the IEC to accept the results would spark yet another crisis for a country that has been paralysed by the two-month delay in settling the election result. Ahead of the announcement, pressure had been mounting on Karzai to accept a possible second-round vote or work out a deal to break the deadlock.

The tainted election has undermined Karzai's credibility and complicated Barack Obama's decision on whether to send more US troops to fight a resurgent Taliban.

The White House has linked the Afghan political crisis to a decision on sending extra US troops to the country. Rahm Emanuel, the White House chief of staff, said the US administration could not make a decision about a request for 40,000 extra troops without a credible government in place in Kabul.

The administration has been delaying a decision on extra troops because of a divide between members of the cabinet, aides, generals and the intelligence services. Emanuel is among those advising the president not to send more troops, partly because of the impact on domestic politics. The war is increasingly unpopular with Afghans.

The US wants Karzai to accept the runoff to establish a semblance of legitimacy. The Obama administration has long privately expressed its lack of faith in Karzai because of the widespread corruption in his government.

Karzai has a fortnight's window to hold a runoff before winter snow makes it impossible.