"There has been great and widespread falsification at the polling stations," Fuad Mustafayev, deputy chairman of the opposition Popular Front Party, told Aljazeera.net.
"We have thousands of incidents documented and they are doing this quite openly and crudely."
However, representatives of the governing New Azerbaijan Party (YAP), led by the president, Ilham Aliyev, deny such allegations.
YAP leaders have repeatedly stated their commitment to holding free and fair elections in the former Soviet republic.
More than 600 observers from the Organisation of Security and Cooperation in Europe (OSCE) monitored Sunday's vote, along with hundreds of local and other international observers.
Preliminary results are expected to start coming in around 8pm (1600 GMT).
The main opposition block, Azadlig, which consists of three parties, including the Popular Front, is to announce its response on Monday morning, with many seeing demonstrations likely.
On a drizzly Sunday in the Azeri capital, Baku, voting was generally subdued.
"I think YAP will win," said one voter, Alik Kuliyev, at a polling booth in the downtown Nasimi and Sabail constituency - where Mustafayev is a candidate.
"But I expect the opposition will also get enough seats in parliament for a balance."
Ali Kerimli, leader of the
opposition Popular Front votes
Few voters spoke of witnessing any intimidation or falsification at this station, yet Mustafayev insists there were many incidents acrss the country.
Another voter, Fakhri Abdulrahimov, was more cautious.
"I think the government has done everything to provide transparency for the election," he said, "but we don't expect the government to provide any transparency when the ballot boxes are shut."
Many Azeris remain sceptical about what will happen to their votes during the count.
In the 2003 presidential elections, there were widespread allegations of fraud and many fear a repeat during this vote count.
"In 2003, before the ballot closed, the opposition thought it had won and began gathering to celebrate," said Suheyla Siyedova from Baku.
"But then government radio announced preliminary results giving the ruling party 70% of the vote in constituencies where people knew it was not possible."
The result was a night of violent clashes between police and opposition supporters in which one protestor died.
Many now fear a repeat performance, if results show similar wide margins between the ruling and opposition parties in constituencies generally thought to be pro-opposition.
Azeri President Ilham Aliyev (C)
after casting his vote
This time, however, there are three exit polls being conducted, two by US firms and one by an Estonian company.
There has also been an effort to combat multiple voting by using invisible ink markers on voters' fingers.
Yet there have been criticisms from the opposition that the ink marking has not been carried out properly.
"In some polling stations they are not following the process," said Mustafayev. "They are not checking people's fingers properly or sometimes at all."