The number of fans arrested for all types of football-related offences in England and Wales rose 8 percent to 3,788 in 2006/7 compared with the previous year.
It was the first rise since 2002/03 when 3,373 people were arrested.
The government said the increase reflected a tougher police approach to antisocial and disorderly behaviour.
Arrests for public disorder leapt to 1,659 from 1,329.
Football attendances increased by 5 percent during the past year to 39 million.
Arrests for racist chanting were down 25 percent at 41, the lowest level on record.
The number of arrests for throwing missiles rose from 68 to 97 after a police crackdown at the beginning of the season.
The Home Office said though that more than 40 percent of all matches were police-free.
"Football violence and disorder has no place in the modern game and we are determined to crack down on those who attempt to ruin the sport for all football fans," said Home Office Minister Vernon Coaker.
"These figures reflect another season of successful partnership work with the police, football authorities, clubs and fans' associations."