Manila police chief Avelino Razon said that a police commander involved in the assault had reported that Alhamser Limbong and Ghalib Andang had been killed.
Heavily armed policemen earlier stormed the maximum security prison in the Philippines capital to end a bloody 24-hour uprising by inmates.
Police swarmed the four-storey building from the gates and from the top floor shortly after 09:00am (0100 GMT) on Tuesday, pouring withering automatic rifle fire on the cells. The assault was shown live on local television.
Some of the 400-plus prisoners on the upper floors could be seen running for cover as tear gas enveloped the Camp Bagong Diwa compound, located inside a police camp in southeastern Manila.
Minutes earlier, government negotiator Parouk Hussin announced the failure of the negotiations to achieve a mass surrender. Nearly a third of them members of the Islamist seperatist group Abu Sayyaf.
Abu Sayyaf prisoners seized the second storey of the building early Monday, killing three prison guards to support calls for better prison conditions and a speedier trial. But the government said the revolt was part of a failed escape attempt.
"A military operation is the next option," said Hussin, governor of a Muslim self-rule area in the south where most of the rioting Abu Sayyaf prisoners came from, shortly before the assault began.
The prison holds many of the top terror suspects in the Philippines, including those blamed for the firebombing of a ferry on Manila Bay last year that claimed more than 100 lives.