Pork DNA has been found in halal chicken sausages served in a primary school in Westminster, central London, the local authority said.
The sausages were from St Mary's Bryanston Square, a Church of England school, Westminster Council said.
Tests on a sample from Burdett Coutts School revealed the presence of lamb and pork DNA in lean minced beef.
The items have been removed from all school meals and the contractor was asked not to use its meat supplier.
Council officers took seven samples in total from three schools in the last week of February to carry out tests on meat products served in schools following the horsemeat scandal.
Halal sausages are served in 15 primary schools, two nurseries, one special school and one pupil referral unit, which take only halal meat.
More than 4,400 pupils choose sausages as a meal option, the council said.
The council said it decided to carry out tests for the presence of DNA from beef, lamb, pork, chicken, turkey, goat and horse after the horsemeat scandal.
No horse DNA was found in the tests.
The Food Standards Agency was alerted by the council on Monday.
Andrew Christie, Westminster City Council's director of children's services, said: "We are very concerned by the discovery that a contractor has fallen short of the high standards we demand.
"We also understand and regret the upset that may have been caused to parents and children alike.
"We are contacting schools, parents and faith group leaders and are offering to meet them to discuss their concerns.
"We have asked our contractor Chartwells to no longer use the meat supplier involved.
"The discovery of pork in these sausages came about because of extra tests Westminster City Council decided to carry out.
"The results were all the more shocking given the assurances about the food we receive from our suppliers. I can assure parents we will keep testing our school meals."
A Defra spokesman said: "It is totally unacceptable if food labelled as halal has been found to contain pork.
"Today Defra, the FSA and the Department for Communities and Local Government met with organisations involved in halal and kosher food to discuss labelling and certification.
"Food manufacturers and suppliers have a responsibility to make sure that the food they serve is what they say it is. The FSA is working with Westminster City Council to establish what happened."
In a separate incident, supermarket Aldi said it has found horse meat in Oakhurst Frozen Meatloaf.
A spokesman said: "Aldi has been contacted by the FSA to alert us that a random sample of our Oakhurst Frozen Meatloaf tested by a local authority has been found to contain horse meat.
"The product is not part of our main range of everyday products and was stocked on a limited availability basis. However, we have immediately withdrawn any of the remaining stock from our stores."