In a television interview, justice GT Nanavati said that the state would not disclose the identity of witnesses if they felt they faced reprisals.
"If there is anyone who feels threatened or intimidated, they should inform us. We will make special arrangements for them, that will ensure that their identity will be protected," Nanavati said.
His comments follow a dramatic admission by a Muslim girl last week that she had lied in a court hearing out of fear of being killed.
Her statement in court led to the acquittal of 21 Hindus accused of burning down her father’s Best Bakery, killing him and 12 others in Baroda town.
She had earlier accused and identified the 21 as the men behind the crime.
Sheikh said she was forced to lie after local Hindu nationalist BJP leaders threatened her.
Backed by human rights activists, Zaheera Sheikh has now called for the reopening of what is called the "Best Bakery case" promising to tell the truth.
Following Sheikh's remarks, several other witnesses have said they would come out with the true story if they were given protection.
The Best Bakery case has been the most high-profile trial since the communal violence that ravaged Gujarat for months last year following the burning in February 2002 of a train carriage carrying 59 Hindus.
First reports alleged that the torching was carried out by a Muslim mob but a subsequent report by forensic scientists in Gujarat in July 2002 concluded that the fire on the train was most likely started from the inside.
About 2,000 people died in the ensuing reprisals against Muslims, according to rights groups. Independent reports blamed the Hindu nationalist state government of orchestrating the violence.
Various human rights groups including the National Human Rights Commission have accused the BJP-led state administration of turning a blind eye to vigilante attacks on Muslims.