Leisure centres and swimming pools in North Hertfordshire face weeks of closures later this year, with costs for decarbonisation works "spiralling out of control" according to one councillor.

An initial budget of around £12.4m for a project to install heat pumps and solar panels – as well as extend the gym at Royston Leisure Centre and refurbishing changing rooms in Letchworth and Royston – has grown to £16.2m. Around £7.7m of the total funding comes from a grant.

On top of rising costs, the council is also now expecting to lose £900,000 in revenue from Hitchin Swimming and Fitness Centre, North Herts Leisure Centre and Royston Leisure Centre while they are closed – a 1,700 per cent increase from a previous estimate of up to £50,000. The costs will be met from the council's reserves.

Leisure centre members will be hit with a number of closures, including at Hitchin Swimming and Fitness Centre where the indoor pool is expected to be closed until 4pm on weekdays for around 21 weeks, and the gym is expected to shut for six months.

It comes after council contractors found that Hitchin Swimming and Fitness Centre does not have a structural deck in its roof, meaning there is "a health and safety risk of materials and people falling through the roof".

Sarah Kingsley, North Herts Council's environment director, told the authority's overview and scrutiny committee on Tuesday (6 May) that they had even considered "pulling the plug" on work at Hitchin.

While the closures have not yet been confirmed, the main pool at North Herts Leisure Centre is expected to be closed for four weeks and the sports hall for 13 weeks. The cafe will also offer only cold food for seven weeks, and the gym will run at a reduced capacity for eleven weeks.

At Royston Leisure Centre, the sports hall will be closed for eight weeks, the gym for four weeks, and the pool for two weeks. There will also be seven weeks where the pool changing rooms will be closed.

The executive member for leisure, Cllr Mick Debenham, said: "While their particular gym or pool is closed, members will not be charged and they will also be able to go to any other Everyone Active site – not just in North Herts but anywhere in the country – free of charge.

 "While we fully appreciate this project will cause some inconvenience to leisure centre customers in the short term, this is a hugely ambitious decarbonisation project which will take us a significant step closer to achieving our climate targets and will also ensure these facilities remain fit for purpose for many years to come."

Work is expected to start at Royston Leisure Centre in July, North Herts Leisure Centre in September, and Hitchin Swimming and Fitness Centre at the end of September.

Cllr Debenham said work at Hitchin could not begin sooner because the council is "waiting on a bat survey", and could not be pushed back further because of the terms of grant funding.

Asked whether the council would have gone ahead with the project at the costs now expected, Cllr Debenham said: "Hindsight is fantastic. It's so difficult to say.

"The whole council thought 'wow, all of our Christmases have come at once, £7.7m has come in.'

"A good news story has turned into a ballache, to be honest with you.

"But I think we're too far down the road now. We've spent the money. You can either just have nothing, or go a little bit extra and get everything."

The leader of the council's Conservative group, Cllr Ralph Muncer, said the project costs "seem to be spiralling out of control" and added that he is "not convinced … that this is the final total".

Cllr Muncer's party colleague, Cllr Martin Prescott, said he was concerned that Willmott Dixon – the construction company that signed a pre-construction services agreement with the council for this project – may "feel they have got a bit of a blank cheque to go wild" with taxpayers' money.

He said that changes to the budget for the project since the original estimate meant the cost to taxpayers had "effectively more than doubled" from an initial £4m.

A Labour member of the committee, Cllr Elizabeth Dennis, said that while she is "concerned about the budget increasing," she continued: "I don't think is going to be this council's HS2 – I do trust our officers and the team we've got working on this to keep oversight of it."

The council's cabinet will need to sign off on changes to the project's budget at a meeting later this month. The decision on awarding the construction contract will also be made.

To date, £6.7m has been spent on the project, including £3.9m on the heat pumps. The council is also already having to pay to store already-ordered building materials at the former Iceland building in Hitchin.