An Australian pilot working in Vanuatu has captured the full scale of Cyclone Pam's destruction in a series of before-and-after photographs.

The category five system hit the Pacific archipelago on March 13 and 14, flattening large swathes of the country.

Captain William Dyer was flying an Air Vanuatu charter flight carrying disaster officials when he took the photographs.

"It's not complete defoliation — there's actually been complete destruction of the jungle in some places," Captain Dyer told Radio Australia's Pacific Beat program.

AFTER: A small island off the south coast of Epi island after Cyclone Pam. ( Supplied: William Dyer )

BEFORE: A small island off the south coast of Epi island before Cyclone Pam. ( Supplied: William Dyer )

The team had been conducting aerial assessments of the Sheppard Islands group in Shefa Province, between the main island of Efate and Epi to the north.

"The Sheppards were hit pretty badly because the terrain is quite steep so there were lots of exposed areas," he said.

"It's made it pretty tough, not just for people living there, but for the ecosystem as well."

The 27-year-old has been flying twin otter aircraft for the national carrier Air Vanuatu for almost two years.

While he has seen several cyclones in that time and said none have caused this much damage.

"I was shocked when I pulled out into the airport parking in Emai [Island] and saw how bad it was," he said.

"I thought I better just take a photo so people can see, because I think it makes it easier to understand just how severe it was if you have the before and after to compare."

AFTER: Emae Island as seen from the air. ( Supplied: William Dyer )

BEFORE: Emae Island in the Sheppard Islands group of Vanuatu. ( Supplied: William Dyer )

He said some of the original photos were taken to send back home to show his family in Queensland how beautiful the country is.

"The photo out the door of the mango tree, I just took it to send the photo home to Mum and say, 'Look you can grab mangoes during the turnaround'," he said.

"It's a very beautiful place and I thought that was pretty cool."

Captain Dyer said he hoped the photos do not send the wrong message to potential tourists.

He said outside of the southern provinces of Shefa and Tafea, much of the country had been relatively unaffected.

"Aside from a few broken branches, [Espiritu] Santo is pretty much like it was before — it's so beautiful," he said.

"It's important people still know it's a nice place to come."

He said he is confident even the worst-affected islands will recover quickly.

"It'll be green again in a couple of months. It won't be the same but it'll be nice again," he said.

BEFORE: A view from the cockpit at Emae airport. ( Supplied: William Dyer )

AFTER: A view from the cockpit at Emae airport. ( Supplied: William Dyer )

Vanuatu's tourism office has advised visitors to delay travel to the capital Port Vila until April 18.

Seventeen hotels are currently operating in the capital but authorities say most rooms are occupied by aid workers.

"There's not a lot of room here at the moment," said Tiffany Carroll, a spokeswoman for Air Vanuatu.

However she emphasised that the tourism industry on the island of Santo, in the north, was operating as normal.

"Don't cancel your holidays. If you're coming to Port Vila or Tanna, go up to Santo instead," she said.

"Definitely don't cancel. We need tourists to return to this country — it's one of the biggest employers in Vanuatu."

Domestic flights in Vanuatu returned to normal schedules on Sunday.

BEFORE: An Air Vanuatu flight to Emae island, south of Epi. ( Supplied: William Dyer )