The court rejected a petition by Bangladesh Nationalist Party (BNP) leader Zia to quash the case, which was filed by a military-backed government, and ordered her to surrender to a trial court within two months.
Zia and 12 others stand accused of costing the state USD 125 million by corruptly awarding contracts to an international firm to handle containers in state-owned depots.
Zia had been trying to get the case thrown out on the grounds that it stemmed from a period of emergency rule and was therefore no longer valid.
"The court asked her (Zia) to surrender before the trial court within two months after she receives the order," he added.
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The leader of the country's largest Islamist party Matiur Rahman Nizami, who is currently on death row after being convicted of war crimes dating back to the 1971 independence conflict, is among Zia's co-accused.
Zia, a two-times former prime minister, has argued that the case is politically motivated and aimed at keeping her out of politics at a time when she is trying to force a fresh general election under a caretaker government.
Zia is already facing four other graft cases and is also being prosecuted for her role in a series of anti-government marches at the start of the year which called for her arch rival Prime Minister Sheikh Hasina to quit.
In recent weeks she has renewed her demand for a new general election under a neutral government, saying Hasina does not have popular mandate to rule following the election last year which was boycotted by the opposition.