Colette Flesch, head of the 72 EU electoral observers who monitored the election, stopped short of endorsing Mr Kagame's landslide victory in Monday's vote, which came nine years after more than half a million people, mostly minority Tutsis, were slaughtered by extremists from the Hutu majority. But she was optimistic about the country's future.
"Optimal conditions for free elections were probably not entirely met," Ms Flesch said. "Nevertheless, this presidential election is the premise for the opening of a new democratic era in Rwanda."
Both government and election officials refused to comment on Ms Flesch's allegations.
At some polling stations, EU observers saw electoral officials tell "voters what candidate they should vote for," Ms Flesch said. At others, Kagame observers simply took over the entire operation and made sure all votes were cast for the incumbent, she said.
The EU observers the largest team monitoring the election visited 372 of the 11,350 polling stations, Ms Flesch said, expressing concern "that even in such a small sample these things could happen".
After voting ended, EU observers were not allowed to monitor the counts, Ms Flesch said.
During the campaign, authorities harassed supporters of Faustin Twagiramungu, the main opposition challenger, she said.
The largely government-run media was biased in Kagame's favour and electoral officials favoured the president, repeatedly castigating Twagiramungu but not addressing the fact that Kagame's Rwandan Patriotic Front party apparently used state funds and gave away hundreds of goats and cows to lure voters, she said.
The picture of the election offered by Ms Flesch stands in sharp contrast to that offered by 19 South African observers who declared the election free and fair.