"The case has been filed against her at the chief metropolitan magistrate's court (Dhaka) this morning along with prayers seeking her arrest," a court official told PTI.
After a brief hearing, the court summoned her to appear before it in person.
"The court summoned her (Zia)... She has been asked to appear by March 3 to face the sedition charge for her recent slanderous comments over the 1971 liberation war martyrs number," another official said.
"There are controversies over how many were martyred in the Liberation War. There are also many books and documents on the controversies," she had said.
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Zia's BNP is a crucial ally of fundamentalist Jamaat-e- Islami, which was opposed to Bangladesh's independence from Pakistan.
The ruling Awami League, 1971 veterans and members of the martyred families had sharply reacted to Zia's comments with some of them even calling her as the "agent of Pakistan".
Today's development came a day after the Home Ministry gave its clearance to move the sedition case against the ex-premier.
The magistrate at that time ordered a police investigation into the allegation and asked the petitioner to obtain government clearance to move the sedition case as required by the law.
The Section 123 (A) suggests one to be "punished with rigorous imprisonment which may extend to ten years and shall also be liable to fine" for "condemnation of the creation of the State (Bangladesh) and advocacy of abolition of its sovereignty".
According to official figures, about three million people were killed during the nine-month long war against Pakistan.
The latest case could compound Zia's legal problems as she is aready facing trial in two graft cases.