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.

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16 November 2014 Last updated at 19:39 GMT
Adam Gilmour was walking to meet a school bus with his mother and siblings when the accident happened near Cloughmills on Tuesday.
BBC Newsline's Conor Macauley reports.

The hosts held a slender 13-11 lead at the break, with Bristol wing David Lemi responding to Will Hurrell's try.
But second-half scores from Ross McMillan and Ben Glynn put the away side, who finished the season top of the table, in command of the tie.
The two teams play the second leg at Ashton Gate on Wednesday, 25 May.
Bristol, who are taking part in the Championship play-offs for the fifth time in seven seasons, elected to play the first leg away from home after losing in the final in each of the last two campaigns.
They are looking to return to the Premiership for the first time since they were relegated in 2009, when they finished bottom with only two wins from 22 matches.
Andy Robinson's team finished 16 points ahead of second-placed Doncaster in the regular season.
Doncaster: Jarvis, Bulumakau, M. Clark, Hurrell, Lewis, Cusack, Heaney, List, Hunter, Quigley, Challinor, Phelan, Makaafi, Hills, Shaw.
Replacements: Veikoso, Brugnara, W. John, Steadman, Young, Flockhart, Field.
Bristol: Arscott, Varndell, Tovey, Mosses, Lemi, Sheedy, Cliff, O'Connell, McMillan, Perenise, Evans, Glynn, Mama, Lam, J. Phillips.
Replacements: Brooker, Traynor, G. Cortes, Sorenson, Robinson, Roberts, Morgan.
Divers in Guernsey will be hit with a £30,000 charge if they require treatment for decompression sickness, the government has confirmed.
[NEXT_CONCEPT]
The funeral of the eight-year-old boy who was killed after his family was knocked down by a car on the way to school has taken place in Glarryford, County Antrim.
[NEXT_CONCEPT]
Bristol took a significant step towards promotion to the Premiership with victory at Doncaster in their Championship play-off final first leg.