The Dhaka court accused Zia and 27 other leaders and officials of her Bangladesh Nationalist Party (BNP) of instigating the petrol bomb attack as part of a deadly anti-government campaign of arson.
"She is the main accused in the case," prosecutor Shah Alam Talukdar told AFP.
Bangladesh ex-PM Zia ordered in court on sedition charge
"The court issued the warrant of arrest against her and 27 other senior officials and activists."
It is not the first time that Zia -- the bitter political rival of Prime Minister Sheikh Hasina -- has faced arrest, and BNP spokesperson Ruhul Kabir Rizvi dismissed the charge as "laughable".
"This is politically motivated and is part of deep conspiracy against her," he said.
The attack took place during a nationwide blockade last year of roads, rail and waterways which Zia called to try to force Hasina to resign and pave the way for new polls.
The blockade unleashed a wave of deadly violence, leaving more than 120 people dead as opposition activists fire-bombed hundreds of buses and trucks and police responded by firing live rounds.
Around 15,000 opposition supporters and dozens of BNP senior officials have been arrested as part of a crackdown by Hasina in the wake of the unrest.
Bangladesh's ex-PM Khaleda Zia gets bail in graft case
A judge in the Dhaka Metropolitan Sessions Court issued the warrant against Zia after accepting a police charge-sheet over the attack in Dhaka on January 10, 2015.
The arrest order is yet another blow to the beleaguered two-times former premier, who has described previous cases against her as politically motivated and aimed at keeping her out of politics.
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