Sheikh Khalifa, 65, has "suffered a stroke that led doctors to operate him... He is in a stable condition," the ministry said in a statement carried by WAM state news agency.
He became president of the United Arab Emirates and ruler of the oil-rich emirate of Abu Dhabi in November 2004, when he succeeded his late father sheikh Zayed bin Sultan, who founded the federation in 1971.
Abu Dhabi sits on the bulk of the UAE's oil wealth, ranked the world's seventh largest, which makes its the wealthiest among the seven UAE sheikhdoms.