Ravji Saundarva, the main complainant, said in the protest petition filed before judge B G Doshi that the central agency did not conduct a proper probe because a BJP MLA was involved.
"CBI has acted as a tool in the hands of MLA Mahendra Mashru," it alleged.
As many as 28 children suffering from thalassemia (a blood disorder) contracted the dreaded HIV infection in 2011 after they were allegedly given blood containing the virus in the transfusions carried out at Junagadh civil hospital.
The probe was handed over to CBI in 2012, which filed a closure report last August, saying that no evidence establishing negligence on the part of the hospital or the blood bank was found.
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"The report claimed no one has done this with intention. But this case is about criminal negligence, not intention," said advocate Paresh Vaghela, representing the parents.
"Based on the statements of witnesses, CBI has stated that Mashru was involved in the day-to-day affairs of not only the blood bank but also the hospital. But since he is a sitting MLA of the ruling party, he was not touched," advocate Vaghela said.