A local watchdog, the Malaysians for Free and Fair Elections, said Sunday’s election was badly managed and the worst ever held since independence in 1957 and should be nullified.
Khairul Anuar, secretary of the watchdog, said on Thursday around 100 volunteers travelled nationwide to observe the election process.
Prime Minister Abd Allah Ahmad Badawi’s ruling National Front won a landslide victory against the Islamic Party (PAS).
Opposition parties had said there were irregularities in the electoral roll that kept thousands of voters from the ballot box.
The Election Commission (EC) was forced to extend voting by two hours in central Selangor state after discrepancies in the rolls saw names of many voters missing from the lists.
Aljazeera's correspondent in Malaysia said the biggest surprise was the routing of the main Islamist opposition, Parti Islam SeMalaysia (PAS).
"This was the surprise, that the Islamist party could be defeated so heavily in its heartlands," said Suhaib Jasim.
"People are still in shock. This is the biggest victory for the ruling party since 1955. Even ex-PM Mahathir Muhammad at the height of his popularity in 1995 could not secure such a big mandate."
PAS retained the state of Kelantan after a recount but lost the neighbouring north-eastern state of Terengganu and was hammered in elections to the federal parliament.
Jasim said that despite isolated demonstrations in the north east he expected the ruling National Front coalition to weather the storm and cement its gains.
The EC also nullified the vote for a state seat in central Pahang and postponed polling to 28 March after a mix-up of party symbols in the ballot papers.
Abd Al-Rashid Abd al-Rahman was quoted as saying he would not step down.
Local newspapers said many angry voters in Selangor left without casting their ballots after queuing for hours to find their names missing from the roll.
"This election is the most chaotic, inefficient and outrageous in the country's history," said Lim Kit Siang, chairman of the opposition Democratic Action Party (DAP).
Abd Allah, who won a resounding endorsement of his five-month rule after taking over from former premier Mahathir Muhammad, has also criticised the EC over the glitches and ordered an investigation.