Thousands of Hindus fled Bangladesh and sought refuge in neighbouring India following the attacks on them.
A judicial inquiry has blamed the violence on supporters of the alliance led by the Bangladesh Nationalist Party (BNP) which came to power in 2001.
The BNP denies the charges, saying they are politically-motivated.
“They want to divert the attention of the people from the failures of this government in almost all social and political sectors,” senior Bangladesh Nationalist Party (BNP) leader Moudud Ahmed told the BBC.
The inquiry was set up about two years ago on the orders of the Bangladesh High Court following complaints by Hindu leaders that there had been a series of attacks against them in 2001, including murder, looting and rape.
They said Islamist parties in the alliance were specifically targeting them because they voted for the rival Awami League in the elections.
The inquiry concluded that more than 25,000 people – including 25 former ministers who are now in the opposition – were responsible for the attacks.
The BNP-led alliance lost power in 2006