Leicester education officials had refused to let Millgate School close for a day to allow staff to attend the funeral of Jane Woolstencroft, who has died of cancer, aged 52.
The school's 28 staff, who teach boys with behavioural difficulties, wrote to the authority saying they were "disgusted and shocked".
"We have been put in an impossible position," they said. "We have been told that if we choose to show our last respects to a well-respected woman, who was employed here for 15 years and passed away while still in service as headteacher, we run the risk of disciplinary action."
The letter triggered Ross Willmott, city council leader, to hold talks with education officials, who agreed to bring in cover staff.
He said: "These are special circumstances and I thought we should do everything we could to help, while not affecting the pupils' education."