Abul Kalam Azad, Zia's spokesman, claimed in TV broadcast that BNP supporters were kept from voting in various parts of the country and said the party intends to file an official complaint.
Bangladeshis turned out in droves to vote in the elections on Monday, which mark the end of two years of emergency rule, instituted due to political unrest.
Election officials and monitors said the polls were mostly peaceful.
The two rival former prime ministers had spent the final day of campaigning criss-crossing the country, promising to lower food prices, tackle armed oppoisiton groups and curb corruption.
Hasina and Zia both said in speeches broadcast on Saturday that it was time to end confrontational politics in which strikes and violent street protests have been common.
|Bangladesh vote: Key facts
Sheikh Hasina Wajed, head of the Awami League and Khaleda Zia, head of the Bangladesh Nationalist Party, are the two main candidates running in the elections.
Both were jailed on corruption charges, but deals have seen them released from custody so they can take part in the vote.
Over 1,500 candidates are running for election, including about 50 women, competing for 300 seats in parliament.
Some 2,000 foreign observers and around 200,000 local monitors are tracking the election process for fairness
About 50,000 soldiers and more than 600,000 police and paramilitary forces will be on duty on election day.
But at mass rallies, they accused each other of corruption, vote-rigging and incompetence, which may set the stage for post-election violence among partisans.
The women, nicknamed the "battling begums" for their intense personal rivalry, have dominated Bangladesh's political scene for the past two decades.
Last year, both Zia and Hasina were jailed on corruption charges, which they dismissed as politically motivated.
They were freed on bail and reassumed positions as the heads of their respective parties.
The impoverished South Asian nation of more than 140 million has a history of questionable elections, sporadic periods of military rule, and politically motivated violence.
But the outgoing army-backed government - which took over in January 2007 and cancelled an election due that month - had said that when it comes to voting procedure and safety, this time things will be different.
Fifty-thousand troops were deployed, as well as 75,000 police and 6,000 members of the elite Rapid Action Battalion (RAB), along with other auxiliary forces for security.
In addition, about 200,000 local and 2,000 foreign monitors were present at polling centres to check procedures.
Waliur Rahman, a former government official, told Al Jazeera that the elections were a "great day for Bangladesh".
|Critics says Khaled Zia's policies are very similar to her rival Sheikh Hasina [Reuters]
"This is akin to a second form of independence day for us. It is a turning point for our nation," he said.
The newly elected government has the daunting task of improving the lives of millions in a country where around 45 per cent of the population live below the poverty line.
While Hasina and Zia alternated in power for 15 years up until 2006, critics say they barely contributed to resolving many of Bangladesh's problems, mainly due to their parties taking to the streets in protests and strikes when out of office.
Analysts also say the women's policy differences are small and to attract much needed investment and aid what matters for Bangladesh is less who wins than that the election brings stability and peace.
"Once the result is known, it is vital that both the victor and the loser - whoever they may be - work together in the interest of the country," said Cassam Uteem, head of the Commonwealth Observer Group.