European Union observers in Kabul yesterday warned that fraud and intimidation were threatening the integrity of the recent Afghan elections. These were held nearly two weeks ago but because of complex logistics, counting is still under way.

"The counting process has revealed worrying cases of fraud, such as ballot stuffing, proxy voting and possible intimidation of voters intended to influence their choice of candidate," the EU election observation mission said.

It urged the joint United Nations-Afghan government body managing the provincial and parliamentary elections to take urgent action before provisional results are announced on Thursday.

"While these phenomena do not appear to be nation-wide, they are a cause for concern," it said. "The election administration [needs] to handle these issues in a transparent and effective way to safeguard the integrity of the electoral process."

Officials working for the former European commissioner Emma Bonino, chief observer, said their statement was a "warning" to the joint electoral management body to examine "crime scene ballot boxes" extremely thoroughly.

One said: "The JEMB must not let its desire for a speedy result come at the expense of the integrity of the process. This is just the tip of the iceberg and it's highly likely there's a similar pattern in other provinces."

Mrs Bonino last month questioned whether a fragmented parliament elected on a non-party basis under a rare choice of voting system backed by the US would produce a "sustainable form of political debate and a healthy political life".

Violence in the south and east prevented the EU, which is funding 40 per cent of the $159m (£90m) poll, from sending its observers to five of Afghanistan's 34 provinces.

The JEMB said yesterday that about 50 per cent of counting was complete and that it aimed to adjudicate all complaints of electoral fraud by October 22, when certified final results are due. Turnout in the parliamentary elections was about 50 per cent, compared with 70 per cent in last year's presidential election.

The lower turnout has been blamed on a baffling ballot paper, poor civic education and sporadic violence.