The workers, who are contracted to build a new facility, at the plant claimed a fire safety drill last Wednesday proved to be inadequate and many workers could not hear the alarm.
They believed there was a safety risk and walked off the site.
It is understood they were told the alarms would replaced on the Thursday and they were asked to go back to work.
But they claimed they were told they would not be paid for the remainder of the day, when the they left the site.
As a result the tradesmen have not returned to work and have staged protests outside the site.
HZI, the main contractor building the new site, said: “Following recent discussions on Ferrybridge Multifuel 2 site, HZI, as principal contractor is in full dialogue with senior stewards and the senior full time officials in an attempt to ensure that the workforce return to work in a timely manner under the conditions of the NAECI agreement.
“HZI would like to stress that from the very first day when concerns were raised they have assured and demonstrated that the HSE concerns raised were taken seriously and ensured that systems throughout the site were fully working.
“This has been endorsed by the unions, stewards and senior officials. We look forward to working together to ensure the safe and timely delivery of the project.”
A spokesman for West Yorkshire Police said: "Motorists please be aware of some traffic disruption on Stranglands Lane, Ferrybridge this morning.
"We have between 500-600 workers out on strike regarding a pay dispute.
"This has caused a great deal of traffic disruption around the former power station site, however we have been working to ensure the road remains open."