Sheikh Khalifa ordered the release of 1,511 prisoners for Ramadan on Tuesday.
The UAE President and Ruler of Abu Dhabi also cleared the debts of the inmates as part of measures marking the holy month.
On Wednesday, Sheikh Mohammed bin Rashid, Vice President and Ruler of Dubai, announced he had pardoned 874 prisoners.
Issam Al Humaidan, Attorney General of Dubai, said their release was allowed in part because of the "exceptional situation the world is currently going through".
Meanwhile, Sheikh Dr Sultan bin Muhammad Al Qasimi, Ruler of Sharjah, also ordered the release of 874 inmates.
Sheikh Hamad bin Mohammed Al Sharqi, Ruler of Fujairah, pardoned 72 prisoners and Sheikh Humaid bin Rashid Al Nuaimi, Ruler of Ajman, released 124.
The Ruler of Umm Al Quwain, Sheikh Saud bin Rashid Al Mualla, pardoned an undisclosed number of prisoners ahead of the holy month while Sheikh Saud bin Saqr Al Qasimi, the Ruler of Ras Al Khaimah released 584.
The Rulers of the Emirates traditionally pardon hundreds of prisoners during Ramadan and other religious holidays.
More than 4,000 inmates were released during the holy month last year.
Those freed are often serving sentences for financial crimes and are chosen because of their good behaviour.
This Thursday, the UAE’s moon-sighting committee will begin looking for the crescent moon that indicates the start of Ramadan.
An official told The National that the committee would meet by video link to discuss when the holy month would start.
The Islamic calendar is determined by moon phases, which are either 29 or 30 days long.
The presence of a new moon signals the start of a new month in the Islamic calendar.
