BNP told the Election Commission that its polling agents had been obstructed in 221 constituencies during the election.
"Our polling agents are being intimidated and obstructed while entering voting stations. In some cases, they are being driven out from the polling stations or being arrested," BNP Joint Secretary General Moazzem Hossain Alal, who led the party's delegation to EC, told reporters.
"We have received the information from reliable sources," he said.
Alal said they were receiving similar complaints from unconfirmed sources from other constituencies as well. He claimed the ruling Awami League activists were committing the irregularities with the help of law enforcement agencies.
The BNP submitted a written complaint, signed by its National Election Conducting Committee Chairman Nazrul Islam Khan, to the chief election commissioner.
The party boycotted the 2014 general election and had been out of office for 10 years.
Alal alleged that voters were not being allowed to enter polling stations in many places and women were being asked to vote for Awami League at the voting centres.
He dubbed the election a "meaningless farce." "It would have been better if a gazette notification was issued declaring the AL winner in 299 constituencies," he said.
'AL stuffing ballots'
The party also accused the ruling Awami League of stuffing ballots on the night before the vote in more than half of the constituencies.
"The ballot papers were stuffed with the help of law enforcement agencies, polling and administration officials," BNP claimed in its written complaint.