The deputy head of the EU monitoring mission, Dimitra Ioannou, said 1.1 million of the suspect votes were in favour of Karzai and 300,000 were cast for Abdullah, a former foreign minister.
'All of them need to be investigated,' she added.
But Karzai, in a statement released by his election team, slammed the election monitor's comments as 'partial, irresponsible and in contradiction with Afghanistan's constitution'.
He stressed that it was up to the ECC to address complaints.
'We believe the only way we can have a legitimate result out of the current process is to allow the legal institutions to complete the process and refrain from interfering in their affairs,' the statement said.
Najafi also echoed Karzai's team demand, saying, 'They (The EU) are observers. Observers can observe the election and prepare a report, they don't have the right to interfere in the election.
'If they have a recommendation, they can submit it to ECC or IEC,' he said, adding, 'They cannot submit complaints, because that is the right of the (Afghan) people.'
ECC said Monday that the final results could take weeks as it was investigating more than 700 complaints that are classified high priority, meaning they are serious enough to affect the outcome.
The exclusion of fraudulent votes from the preliminary results could drag Karzai's share of the vote to below 50 percent and force a run-off with his top challenger Abdullah. A run-off could be held around the end of October or the beginning of November.