5 million votes, or a quarter of all ballots, had been manipulated or were suspected of having been subjected to tampering.
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.
Karzai said Thursday that he was 'shocked' by the numbers but that any charges of irregularities would be investigated by the Election Complaints Commission.
On Wednesday, he had called the EU findings 'partial, irresponsible and in contradiction with Afghanistan's constitution'.