President Sheikh Khalifa ordered the release of 645 prisoners on Monday ahead of the UAE's 46th National Day.
He also pledged to pay off their financial obligations in a bid to give them an opportunity to start a new life and ease the suffering of their families.
Sheikh Mohammed bin Rashid also ordered the release of 606 inmates on Monday.
Issam Al Humaidan, Attorney-General of Dubai, said the Vice President and Ruler of Dubai took the occasion to issue the amnesty order to give the prisoners an opportunity to re-engage in society.
Mr Al Humaidan said the Public Prosecution is coordinating with Dubai Police General Command to carry out the order.
Sheikh Saud bin Saqr Al Qasimi, Ruler of Ras Al Khaimah, pardoned 246 prisoners from the emirate's punitive and corrective institutions to mark Commemoration Day and National Day. He too pledged to settle the financial debts of those pardoned.
Sheikh Mohammed bin Saud, Crown Prince of Ras Al Khaimah, instructed the chairman of the RAK Judicial Council to take necessary measures to implement the orders in co-ordination with RAK Police.
Every year ahead of religious holidays, the president and rulers of the emirates pardon prisoners and order the settling of debts, which prevent many from leaving prison.
Last year Sheikh Khalifa ordered the release of 1,102 prisoners to mark National Day.