"The Medical Research Institute has been asked to prepare menus that could be used for alms givings," the ministry said in a statement, adding that the new guidelines would be issued next month.
"The food that is offered is tasty and very rich and it causes immense health problems for monks," it said.
There are over 40,000 monks in Sri Lanka, where Buddhism is the religion of the majority of the nation's 20 million people. Offering food to monks is believed to bring good luck in this life as well as in the next.
Buddhists who believe in reincarnation also offer food to monks in a bid to transfer good karma or fortune to departed loved ones.The offering of breakfast or lunch requires much preparation and temples are usually overbooked. Devotees must sometimes wait for a year to get a slot in the alms calendar of a temple.
While monks in urban areas have no shortage of alms, several temples in remote areas have closed down due to a lack of support from impoverished villagers.
The health ministry said it was also setting aside separate wards in every state hospital to treat Buddhist monks as well as other clergy.