Changes to the Health Legislation Amendment (Information Sharing) Bill have been agreed to by the Andrews government following talks with the upper house crossbench.
The bill will enable public hospitals and other health services to more easily share patient information through a centralised database.
Domestic violence survivors, legal practitioners, civil liberty groups and cyber experts have voiced fears personal information could fall into the wrong hands if the database is hacked or inappropriately accessed by health staff.
Several crossbenchers flagged they would not support the bill, with Labor needing the votes of at least six non-government members for it to pass on Thursday.
Facing the prospect of defeat, the Andrews government agreed to mandate a privacy management framework and independent expert review of the system after two years.
"These amendments reinforce the protections already in the proposed legislation by further strengthening transparency and accountability of the new secure, digital health information sharing system," a government spokesman said.
Victorian Greens acting health spokesman Tim Read said the party was set to support the bill, pending further government assurances.
"Our public hospital system is struggling with staff shortages and delays, but giving them this system will mean staff waste less time on the phone and can spend more time seeing patients," he said.
But the Law Institute of Victoria remains unmoved in its position, declaring people must have the ability to opt out.
"We are not saying 'no' to a health information sharing scheme, only that Victorians deserve a choice," its president Tania Wolff said in a statement.
Opposition health spokeswoman Georgie Crozier moved amendments on Tuesday to create an opt-out clause, similar to the federal government's My Health Record scheme.
During an at-times fierce debate, Liberal MP Wendy Lovell noted there have been high profile cases of officers inappropriately accessing Victoria Police's central database.
"We don't want that happening with health records in Victoria," she said.
Animal Justice Party MP Georgie Purcell said her support for the bill hinges on the addition of better privacy protections rather than an opt-out provision.
She was waiting to read the government's amendments before committing her support, while David Ettershank said he and fellow Legalise Cannabis MP Rachel Payne also shared concerns on patient confidentiality.
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