Final results are expected to be announced at noon (1100 GMT) on Monday.
"The final result might not fully reflect the will that was expressed by the people of Angola in the ballot," Isaias Samakuva, Unita's leader, said on Sunday.
Unita has lodged a complaint with Angola's electoral commission over the running of the vote.
Angola's parliamentary election uses a variation of proportional representation, with seats allocated based on results from the national and provincial levels.
Voting began on Friday but was extended into Saturday because of delays and confusion at polling stations in Luanda province, home to 21 per cent of Angola's 8.3 million registered voters.
A disputed poll could shatter the fragile political stability that has existed since the end of a 27-year civil war in 2002.
"We have no choice but to file [a] challenge. Conditions did not exist for the election in Luanda yesterday and they still do not exist today," Adalberto da Costa, a Unita spokesperson, said on Saturday.
The government has denied any electoral wrongdoing, while admitting that there had been administrative glitches in some areas, particularly around Luanda.
MPLA spokesman Norberto dos Santos said Unita's legal battle is without merit.
The MPLA had been widely expected to win the election, but the partial results suggest the party is within reach of the coveted two-thirds majority that would allow it to make sweeping changes to the country's constitution.
The MPLA held 129 of the 220 seats in parliament heading into the election, with the remainder controlled by Unita and a handful of smaller parties.
Unita's Samakuva has expressed doubts about the credibility of the poll [AFP]
Problems with voter registration lists have been cited as the main cause of the delays on Friday.
"The law was broken because the electoral registration was not distributed," Luisa Morgantini, who is leading a 120-member EU team, said.
"We cannot say the process was done according to the rules," he said.
Morgantini, after meeting Angolan election officials, later said she was pleased with their efforts and impressed by the way in which Angolans had cast their votes.
An observer mission from the Southern African Development Community (Sadc), a 15-nation group that includes Angola, said on Saturday the election was credible, free and transparent, according to Angola's state-run Angop news agency.
But Isaias Samakuva, Unita's leader, has described the poll as a "mess" has threatened to refer a claim to the constitutional court.
Tensions between Unita and the MPLA have simmered since the opposition group ended its war against the state six years ago.
In the run-up to the poll, Unita accused the MPLA of using state funds for its campaign and the state-run media to publicise its cause.
It also said its supporters had been harassed, a charge backed by US-based Human Rights Watch.
Independent Angolan election observers said on Saturday that the voting was largely free of violence and irregularities, but that it was too early to declare the poll legitimate.
Angola's government has touted the poll as a showcase for its recovery from the civil war and hopes that it will spur further foreign investment.
Stefanie Dekker, Al Jazeera's correspondent in Luanda, spoke to locals who say they should simply accept the results because after six years of peace no one is in the mood to return to armed conflict.
"Even though many people here want these elections to go smoothly, the main opposition party has not accepted these elections, and international observers have yet to give their stamp of approval," Dekker said.
Angola rivals Nigeria as sub-Saharan Africa's biggest oil producer.