A spokeswoman told HR magazine: "We do not know where the GMB is getting this figure from. We have asked them to substantiate it and they have not. Salaried pay and pensionable pay will be unaffected."
In April the company asked maintenance workers to change their hours from 8am until 4pm to 10am until 6pm once every five weeks. Anglian Water has already carried out trials of changes to shifts in other parts of the organisation with success.
The GMB balloted its members who carry out maintenance work for the water company on the changes and it has been decided GMB members will withdraw goodwill services from Monday 8 June and take part in a 24-hour strike on Friday 12 June.
Anglian Water "emphatically denies" GMB accusations that its HR manager, Kate Kelly, "told GMB members to go on strike if they did not like the new imposed terms".
The spokeswoman told HR magazine: "This is a gross misrepresentation and [Kelly] certainly did not say this. We have 4,000 members of staff and only 85 [of 235 entitled to ballot] voted in favour of this strike."
The company is unsure how many employees will take part in next week's industrial action but, in a statement, emphasised there would be no adverse effect on water services.
Peter Simpson, chief operating officer at Anglian Water, said: "The dispute is about a minor change to start times. We're asking staff to start work at 10am instead of 8am to ensure we have most cover available when we are busiest. Many of our staff already work to these new arrangements.
"Since the new arrangements began on 1 April we've improved service to customers and reduced the use of outside contractors by 40%. This kind of efficiency improvement can only be good for our customers' bills and the long-term job security of our employees.
"We remain absolutely committed to consulting our staff on changes that affect them, and we're proud of our track record for constructive employee relations. The fact is we have negotiated on this change in good faith for more than eight months, but sadly it was not possible to reach agreement.
"We urge union members to step back from strike action and to agree to the new working arrangements."
This latest announcement of a strike action follows news of industrial action on the London Underground on 9 June by the Rail, Maritime and Transport Union.
Anglian Water denies trade union claims of pay cuts in the face of industrial action
Staff at Anglian Water are set to strike next week over trade union claims of potential pay cuts and changes to shift patterns but Anglian Water denies claims by the GMB union that staff could lose as much as 2,500 per year in pay.