The hyperbaric chamber, which treats divers with "the bends", was operated by St John's Ambulance on a donation basis until it broke in April 2014.
The health department replaced it in 2015, but says it needs to "balance the books".
Diving instructor Steve Bougourd said he was "gobsmacked".
"I'm just worried that this kind of cost will put people off of actually going to the [hospital] and notifying them if they suspect a problem," he said.
"We may find it's going to be very expensive to get out divers insured."
In the UK hyperbaric oxygen treatment is covered by the NHS, but Guernsey has its own health care system.
Source: NHS
Assistant director at Guernsey's health and social care department (HSC) Ed Freestone said renting the chamber was costing the government £60,000 a year.
He said the department would not make a profit from the new charges, which were based on "the average usage that we could identify over the previous few years".
In addition to paying for the training of staff and the maintenance of a 24 hour service, the department had to fund plans to buy its own chamber for about £250,000, Mr Freestone said.
Commercial divers already pay a £150 notification fee to dive which raises about £10,000 a year, according to HSC.
It is a legal requirement to provide a hyperbaric chamber facility for commercial diving activity to take place within Guernsey's 12-mile limit.
Divers in Guernsey will be hit with a £30,000 charge if they require treatment for decompression sickness, the government has confirmed.