HALIFAX -- This is the time of year when many pharmacies have parking-lot signs promoting the flu shot. But this year some of those signs have the opposite message.

The vaccine is still in short supply in some areas and one pharmacy on Joseph Howe Drive in Halifax posted a sign outside saying "Waiting for vaccine supplies."

In Dartmouth, another pharmacy has put up notices in store, linking customers to a vaccine availability website.

"We didn't get quite as much vaccine at the start of the program as we usually get, so that's led to a few issues with some vaccine providers," said Nova Scotia Chief Medical Officer of Health Robert Strang.

Some pharmacies and doctors' offices do have the flu vaccine, but you'll have to wait.

"It was a 45-minute wait, and after you have the shot it's another 15 minutes, so you're looking at 45 plus 15 minutes," said Jack Campbell. "There were five people in line there waiting."

Said Paula McSweeny: "It's going to be a long wait every time you come in, so you might as well stay and wait. You have to get it done."

Suzanne Bertin knew there was a shortage but she was already going in for a blood test.

"I asked, 'Are the flu shots out?' and she said, 'Yes, they are,' so I figured I might as well get that done too," Bertin said.

New Brunswick faced a similar situation last week when the Health Department said it was also waiting for vaccine and expected to have 90 per cent of its supply by the end of this week.

The Nova Scotia Health Department says they have about 88 per cent of the vaccine they ordered.

They expect to get the full dose by the end of next week and they have this message for vaccine providers:

"Don't expect to get all the vaccine that you think you need, and to immunize all the people you want to immunize in the first week or two," Strang said.

The vaccine this year covers multiple flu strains, including h1n1 and h3n2. Flu-shot season lasts for the next two months.

With files from CTV Atlantic's Emily Baron Cadloff.