A total of 7,750 households were still without a water supply on Tuesday morning, up from 6,500 on Monday morning.
Problems at the Lough Bradan water treatment works are behind the latest supply disruptions in West Tyrone.
The fresh supply disruptions come just a week after the company said that 10,000 customers in the Fermanagh and Tyrone areas were without a mains water supply following a fault at the Enniskillen treatment plant which had suffered delays in being repaired.
The water service provider said it anticipates more customers will experience disruption throughout the day as the disagreement which began late last year, remains unresolved.
Union members have withdrawn from overtime and on-call work and NI Water said that due to “limited resources” as a result of the industrial action, its response has “been restricted”.
The company said interruptions to customers were “virtually inevitable” due to the 26,000km of water mains, 15,000km of sewers and thousands of pumping stations and treatment works which need to be monitored.
In a statement, NI Water said that it is “working to minimise disruption to customers’ supplies” and will “provide alternative supplies” wherever possible and suggested customers “use water wisely to help conserve remaining supplies”.
The company said it remains on “high alert” and continues to engage with trade unions in an effort to resolve the dispute.
More than 1,000 members of the trade unions started industrial action on 22 December because of changes to the pension scheme, which the GMB claims will cost members up to £100 per month. A pay deal offered by the company was rejected last week.