The opposition groups also charged that the investigations were rigged.
The government and the National Electoral Board have rejected the charges.
Brehanu Nega of the main opposition Coalition for Unity and Democracy said on Tuesday the government and the National Electoral Board had rigged from the start investigations into irregularities in 139 of the 524 seat contested in the 15 May polls.
The investigations began after police shot dead at least 40 people and injured dozens during last month's protests against alleged electoral fraud.
The opposition groups said more than 90% of their complaints have been rejected and the vote had gone in favour of the ruling party.
"The investigation process was a complete failure," Brehanu told journalists in Ethiopia's capital, Addis Ababa. "The environment in which the panels conducted the investigation was too flawed to ascertain that there was vote rigging.
"Our representatives and witnesses have been harassed, threatened, barred and killed upon their returning from the hearings"
Brehanu Nega, Coalition for Unity and Democracy
"Our representatives and witnesses have been harassed, threatened, barred and killed upon their returning from the hearings," he said.
Beyene Petros of the opposition United Ethiopian Democratic Front said attempts to undermine the investigations could threaten the calm restored after last month's unrest.
Ruling party favouritism
"More than 90% of these constituencies where we submitted complaints, the workings have been irregular and favour the ruling party," he said.
Information Minister Bereket Simon accused the opposition parties of trying to undermine the process with their allegations, which he said were unfounded.
"The investigations have taken place in the presence of international observers," the minister said. "We believe that the process is moving on the right path, is on track, transparent and open."
Electoral board spokesman Getahun Amogne said: "The investigations have been following proper procedures and we are not biased in favour of any political group."
Claims of fraud
On 8 July, officials released results for more than half the seats, showing the ruling party and opposition in a virtual tie. Results for the remaining seats, however, were delayed as officials checked claims of fraud.
Opposition parties have fared
creditably in the 15 May polls
The ruling Ethiopian People's Revolutionary Democratic Front and its smaller political allies have won 158 seats to 148 seats for the opposition coalitions in the 547-seat parliament.
Results for the remaining seats will be released on Friday after officials wrap up investigations. Most of that work has been completed and the board has received findings from 80 constituencies and are waiting for 60 to come in, Getahun said.