Candidates caught with mobile phones in exam halls accounted for around 25 percent of the offenses, the Qualifications and Curriculum Authority (QCA) said.
"Over recent years we have seen ain examination halls across the country," said QCA Chief Executive Ken Boston.
Students can be marked down or even failed for just having a mobile phone with them during exams, whether they use them to cheat or not.
Boston said he would be writing to all schools about the importance of students leaving their phones outside exam halls.
Just over 4,500 students were penalized during last summer's round of A-level and GCSE exams, a rise of 27 percent over the previous year.
However, the overall number of candidates penalized remains low, with less than one incident for every 1,500 exams taken.
Around one-third of the offenses involved students caught for plagiarism, collusion or copying another candidate's work, typically in coursework done before a final exam.
Others were penalized for cheating or disruptive behavior during exams, writing obscenities on their exam papers or failing to follow instructions.