Under the terms of a US-Taliban deal, Kabul pledged to free some 5,000 Taliban prisoners in a swap that would see the insurgents release around 1,000 Afghan security force captives.
But National Security Council (NSC) spokesman Javid Faisal told AFP that 600 prisoners the Taliban asked to be freed still had "serious criminal cases" against them.
They include people charged with murder, highway robbery and even sodomy, as well as hundreds of foreign fighters, another government official said on condition of anonymity.
"They are too dangerous to be released," the official said.
The Taliban on Wednesday accused the government of fabricating criminal cases against the prisoners.
"If they continue to create more problems in this regard, then it shows they do not want issues to be solved through reasonable ways," spokesman Zabihullah Mujahid said.
But NSC spokesman Faisal insisted the government was committed to the talks.
"We are ready for peace and will release the remaining prisoners... as per the agreement -- just not these hundreds of prisoners who have serious criminal cases in the courts," he said.
Both sides have pledged to hold direct talks aimed at ending the decades-old conflict in Afghanistan after completing the exchange.
The government has already freed more than 4,000 Taliban fighters, while the insurgents have completed around two-thirds of their releases.
Earlier this week a top Afghan official said it was up to the authorities to decide who should be released.
"We don’t expect the Taliban to tell us which inmates to be released," said Sediq Sediqqi, spokesman for President Ashraf Ghani.