There was no immediate claim of responsibility for the triple attack but Britain-based war monitor the Syrian Observatory for Human Rights said sleeper cells of the Islamic State group were probably responsible.
The ministry said that the targets included the oil refinery in Homs, one of only two in Syria, and two gas facilities, one south of the city and one in the desert to its east.
The ministry said that several production units had been damaged and repair teams were working alongside firefighters to try to restore output as quickly as possible.
Government-held areas of Syria suffer from a chronic shortage of fuel, partly because of Western sanctions on crude imports and partly because the largest oil and gas fields lie in the east, which remains under the control of US-backed Kurdish forces.
Observatory director Rami Abdel Rahman said he believed the attacks were the work of IS, which has proved it remains capable of operating in both government- and Kurdish-held areas despite its loss of the last redoubt of its self-proclaimed caliphate to Kurdish forces in March.
A few hours earlier, IS fighters had attacked an army garrison in a gas facility east of Homs, killing four civilians and 13 troops or militiamen, the Observatory said.
Follow us on Twitter and Instagram to stay connected