The Boston public schools ousted their longtime director of food and nutrition services yesterday after finding 280 cases of out-of-date food in 40 cafeterias amid allegations from a city councilor of systemic mismanagement and widespread waste.

School officials said they have set aside 3,049 more cases of food, worth roughly $107,000, in a privately operated supply warehouse in Wilmington because records do not readily show expiration dates or “best-if-used-by’’ dates. Officials are peeling away plastic packaging on the pallets, looking for dates or other clues to how long the food has been in storage.

US Department of Agriculture guidelines say that properly frozen food can remain safe after expiration dates, but that it can deteriorate in taste and nutritional value. A USDA spokeswoman said yesterday that the department urges food service officials to “err on the side of caution,’’ especially when serving children.

Deputy School Superintendent Michael J. Goar acknowledged problems in Boston’s food management yesterday, saying, “This clearly highlights that we need to do a better job with inventory control, as well as better menu planning.’’

Goar said the discoveries do not necessarily mean that students have been served food that has been in storage past expiration dates.

“Just because you have [out of date food], does not mean you are going to use it,’’ he said. “I don’t want people to say there is food from 2008 being used to feed our kids. That is far from the truth.’’

But Councilor at Large John R. Connolly, who found out-of-date food in freezers at four school cafeterias in surprise visits earlier this month, said he has found documents that suggest high schools served frozen grilled egg patties in January that had been bought during the 2008-2009 school year. The School Department disputed Connolly’s interpretation of the documents, but officials acknowledged that there is no way to accurately determine the age of food from their invoices. The same records appear to show that the department routinely ordered food items, such as chicken patties, that it already had in abundance in storage, Connolly said.

The warehouse, Wilmington Cold Storage, charged the city more than $73,000 last year for storage and other services. School officials are responsible for ordering food stored there.

“Poor inventory management led to Boston public schools paying to store food and serving expired food to our students,’’ Connolly said yesterday as he and his staff examined five boxes of menus, inventories, and other documents from the department. “It’s totally unacceptable.’’