Two judges of a High Court bench delivered dissenting orders on the petition of the 68-year-old Bangladesh Nationalist Party (BNP) chief.
Justice Farah Mahbub stayed the trial proceedings of both the cases for three months and issued a notice to the government to explain why the appointment of Judge Basudeb Roy should not be declared illegal.
In line with the practice of the High Court, the matter will now be forwarded to the Chief Justice who could refer it to a third judge of the High Court for settling the issue.
The two-time former premier, Zia filed the petition on May 12 challenging her indictment and the appointment of Justice Roy, citing procedural flaws and sought a stay order on the proceedings of the corruption cases.
On March 19, Roy indicted Zia in 'Zia Charity Trust and 'Zia Orphanage Trust' graft cases involving over USD 6,50,000.
Justice Roy fixed June 19 as the next date of hearing, accepting a defence plea seeking more time.
Zia last appeared before the court on March 19 when charges were framed against her, her "fugitive" elder son and BNP's senior vice president Tarique Rahman in the cases filed by the Anti-Corruption Commission (ACC).
Zia's repeated absence in the court had forced deferment of arguments for 41 times in the past three years.
In August 2011, the ACC sued Zia and three others for siphoning off 31.5 million taka (about USD 4,00,000) from the Zia Charitable Trust.
The two charities were named after Zia's late husband Ziaur Rahman, a former president who was assassinated in 1981.
The charges date back to Zia's last term as premier from 2001 to 2006 and can carry a life sentence, prosecutors said.
Zia's lawyers have called the charges politically motivated aimed at destroying the main opposition party which has vowed to topple the government of her arch rival Prime Minister Sheikh Hasina.
Zia was indicted just weeks after the ruling Awami League came to power after the January 5 general election which was boycotted by BNP and its 18 opposition allies.
