Doctors Nova Scotia has apologized to physicians over the way it handled a side deal that gave a 21 per cent pay hike to Halifax-area emergency room doctors while other doctors accepted a one per cent raise.

"I understand that many of you are confused and upset, and that you may feel that Doctors Nova Scotia does not effectively represent your interests," new president John Chiasson said in a June 8 letter to doctors, obtained by CBC News on Friday.

He said the deal was negotiated last December before doctors agreed to reopen their master agreement in the name of austerity. That saw doctors accept a one per cent pay increase in line with other Nova Scotia government wage settlements.

Chiasson's letter addresses concerns that the media learned about the emergency room funding first, saying "this was not appropriate and I apologize."

"In the media this contract has been presented as new, which is not the case. It appears this way because of the lengthy bureaucratic process," Chaisson wrote.

The 21 per cent increase boosts ER doctors pay to $190 an hour, up from $156 per hour.

Other doctors will also get bigger pay hike

Chiasson said the money to give pay raises to emergency room doctors at the IWK Health Centre and the Queen Elizabeth II Health Sciences Centre in Halifax comes from last year's budget and is retroactive to April 2010.

The letter also revealed that four other physician groups will receive additional money beyond the one per cent increase announced earlier this year.

Pathologists, psychiatrists and emergency room doctors who work in rural centres will also see retroactive raises from the 2010 budget year, according to Chiasson's letter.

Doctors Nova Scotia told CBC News Friday that psychiatrists in rural areas saw their pay boosted from $135 to $142 an hour — a 4.5 to five per cent increase.

Pay boosts for rural ER doctors and pathologists have not been finalized.

Doctors Nova Scotia also told CBC News on Friday that 180 specialists in metro Halifax who are being paid on a fee for service basis will get $10,000 in a lump sum payment over two years.

Kevin Chapman, director of health policy and economics, said these payments are allowed for in the master agreement between the province and doctors.

"This is flexibility to address pressure points where we need to attract and retain physicians," Chapman told CBC News.

The province is working on another five side deals with other physician groups.

In his letter to doctors, Chiasson said he wanted to clear the air.

"From some of the comments I've received, it's clear that when we have a win for one group of physicians, it's often perceived as a loss for another group," he wrote.

"What you should know is that we are always trying to treat our members fairly and represent them as best we possibly can. I make no apology for our commitment to advocate for fair and equitable compensation for the work we do."