"They are making a lot of money out of penalty fees," said Linda Field, the school's exams officer. "It feels like punishment."
Another school was fined pound;75,000 for filing almost all of its registrations late, according to a cautionary tale told by National Assessment Agency officials.
Exam boards say late fees are necessary to ensure assessment and marking run to schedule, but some school leaders say the penalty fees are punitive and money-grabbing.
Last year, schools and FE colleges were penalised for more than 700,000 late entries, costing them an estimated pound;10 million to pound;20m.
Malcolm Trobe, president of the Association of School and College Leaders, said the penalty fees posed a "real financial problem" for schools if they had difficulities.
But the National Assessment Agency argued that the improvement on 2005, when there were more than 1,000,000 late entries, showed that penalty fees were getting the message across.
The exam boards agreed: three of the biggest, Edexcel, OCR and AQA, issued a joint statement saying penalty fees were used to reduce the number of late entries and to cover the additional administrative costs. But they refused to disclose how much they were fining schools each year, citing commercial sensitivity.
At William Morris sixth form college, in Hammersmith, Ms Field said entry rules were complex and differed from one exam board to the next, meaning the potential for mistakes was vast.
She complained to Edexcel after the school was fined pound;6,600 last year. Eventually, the board agreed to halve the fine to pound;3,300, "as a gesture of goodwill".
An Edexcel spokeswoman advised schools such as William Morris to phone the board if they were experiencing difficulties.