Hundreds of nurses at Craigavon Hospital, Daisy Hill in Newry and across Northern Ireland taking part in a 12 hour strike
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The strike, from 8am to 8pm, is over fair pay and staffing issues.
Hundreds of hospital appointments have been cancelled due to the strike which is the second day of strike action.
Emergency departments will continue but other services will be disrupted.
The Royal College of Nursing (RCN) warned of further strikes in the new year.
The RCN, representing about 500,000 nurses across the UK, say its members should have a pay rise of 5% over RPI inflation, which amounts to a rise of 19%.
The government appears to be no closer to making a deal on pay for nurses, describing the 19% as ‘unaffordable’.
Peter May is the most senior civil servant working within the Department of Health, and is currently heading the department up in the absence of Stormont ministers.
Speaking to BBC Spotlight for their ‘Inside A&E’ programme – which spent two days filming at Craigavon Area Hospital, Mr May ruled out additional funding for social care to ease emergency department overcrowding.
He said: “Our health and social care system is in trouble and it needs help at the moment.”
In relation to the overcrowding issue in NI’s hospitals, he added that former health minister Robin Swann had increased funding for social care, to some benefit, but there was currently no scope for a further boost.
"We're fighting to live within the budget that we've been set, we have a serious, significant amount of savings to make during the rest of the year to live within that budget," he said.
"There isn't a pot of money sitting there ready to be allocated to social care."
The Southern Health Trust's chief executive Maria O'Kane told the show she was disappointed Mr May had ruled out additional funding.
"I think it puts all of us in health in a really difficult position because effectively what we're being asked to do is more for the same and potentially less," she said.
"But, at the same time, we are very aware there's not enough currently to balance the books."