Police laid initial charges against the former two-time premier over Tuesday's attack, the deadliest incidence of violence since the month-long protests started.
"She has been named as an instigator of the attack. At least 56 other people were also charged in the case," district police chief Tutul Chakrabarty told AFP.
Police also arrested around a dozen protesters, accusing them of carrying out the attack as part of an opposition-led nationwide transport blockade.
The charges are the latest for 69-year-old Zia, whom police said last week was also under investigation for "abetting" and "instigating" other recent firebombings.
There is no immediate comment from Zia or her Bangladesh Nationalist Party (BNP) which has condemned Tuesday's attack and denied its supporters were responsible.
Authorities have stepped up pressure on Zia, who has been holed up in her office since January 3, in a bid to halt the violence.
At least 54 people have been killed -- most victims of firebombings of buses, cars and lorries - as activists try to enforce the blockade of roads, railways and waterways.
Zia called the protests early last month to force Prime Minister Sheikh Hasina to call a fresh election. The BNP and its allies boycotted the January 2014 poll on the grounds they believed the result would be rigged.
Security forces have launched a nationwide crackdown, arresting more than 10,000 opposition activists since the blockade began.
Hasina has accused Zia of trying to trigger "anarchy" and ordered security agencies to hunt down the protesters.
The EU, the nation's biggest export destination, has urged Hasina's government and the opposition to hold talks to resolve the crisis.
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