Northern Football Federation football development officer Dave Alabaster said knee injuries were most common, along with ankle sprains, and broken arms or legs.
Fifa has designed a football injury prevention programme called Fifa 11+, which has been rolled out in New Zealand in conjunction with New Zealand Football.
The extensive warm up programme aims to reduce injuries in players aged 14 years and over, although it is up to individual clubs to take it on board.
Mr Alabaster said the programme was used with the federation's high performance players, but local clubs were yet to take it on to a great extent.
"It's about to become a big focus."
Many parents preferred to enrol kids in football than rugby because of safety fears, he said.
"Anecdotally we hear of a lot of kids that come to football because parents are unhappy with the physicality of rugby."
He estimated about 3500 football players were registered in Northland, although rugby had double that number with 7001 in 2012/13.
Events such as the Fifa World Cup, which is currently taking place in Brazil, and next year's Under-20 World Cup, which New Zealand is hosting, helped to boost the game's profile and could increase player numbers by 5-10 per cent.
The Under-20 World Cup would have more of a local impact because games were scheduled in Whangarei, he said.
Physiotherapist Hamish Aston, who has experience with international football teams, said the main injuries he dealt with were ankle injuries from tackling, hamstring strains from running, and the occasional knee injury.
Early in the season it was more common to see shin splint injuries from running on hard ground, and as the ground got muddier more players were prone to tired muscles.
He was seeing more elite junior players in the 12-16 year old age group who were "over-worked and over-trained", but it was hard to predict what impact their injuries would have on their sporting future.
"They've got growing bodies and they're doing almost professional workloads ... and they've got to do their school work and everything on top of that.
He was concerned at a lack of awareness and funding around football injury prevention programmes, but was an advocate of the Fifa 11+ programme.
"If teams do it regularly and properly it's shown to reduce lower limb injuries by 40-50 per cent."