A fire at an important election centre in Kinshasa, on Thursday has increased suspicions over the transparency of the results.
Used and unused ballots were among the material burned in the centre that was due to process one quarter of the capital’s votes.
Voting took place amid relative calm on Sunday but the days after the poll, which cost over $450million to organise and was protected by the UN's largest peacekeeping mission, have been marked by complaints and threats of challenges to the results.
At the election centre in the neighbourhood of N'Djili, workers said they had burned empty ballot boxes to clear up rubbish.
But a Reuters reporter saw the remains of burned ballot papers, some used, others unused, in the ashes outside a room littered with voting material.
One foreign election observer said: "It would appear that something serious has taken place here. The key question is what is the size of the problem?"
Election officials at the office were due to process votes coming from 1,400 polling stations before passing them to compilation centres for cross-checking and safekeeping in case the results are challenged.
Congo's independent election commission was not immediately available for comment.
Counting votes from 50,000
polling stations takes time
One of Congo's former rebel groups has complained of fraud during the polls. A major opposition party boycotted the election saying it would not be free and fair.
Observers said the voting might have gone well on the day but that the process of collecting results from some 50,000 polling stations would be time-consuming and had become chaotic.
Meanwhile a senior commander of EU troops in the country warned against the use of force to challenge the results of the elections.
Colonel David Pincet said the EU mission (known as Eufor) had the "means to dissuade" anyone using force to contest the results, as it emerged that a Eufor drone that crashed over Kinshasa last week while monitoring the polls had been deliberately shot down.
Joseph Kabila, the incumbent president, is the slight favourite to win the vote which was contested by 32 candidates.
Elsewhere in Congo on Thursday 17 people were killed when a plane crashed due to bad weather in the east of the country.
The Antonov 28 plane was flying in low cloud as it approached the airport at Bukavu in the South Kivu province when it clipped a mountainside and plunged into the forest in flames. A UN spokeswoman said all fourteen passengers and three crew were killed.