Skybus said despite the forecast it was "hopeful" all its scheduled flights would go ahead.
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The Isles of Scilly Steamship Company runs the Skybus service and the Scillonian ferry.
The company's fleet of Skybus aircraft would increase from six to seven, they added.
Land's End Airport is closed until Thursday because of a waterlogged grass runway, preventing Skybus flights.
Skybus operator, the Isles of Scilly Steam Ship Company, is flying from Newquay Airport in the meantime.
Skybus already has three of the 19-seater Twin Otters in its fleet, plus three eight-seater Britten Norman Islanders.
The Isles of Scilly Steam Ship Company's Skybus service said the matting would help to "reinforce the surface".
The Scillonian ferry currently runs for only seven months a year and the other link, Skybus, is weather-dependent.
The Isles of Scilly Steamship Company is responsible for both the Scillonian ferry and the Skybus plane links to the islands.
The work has been carried out by the Isles of Scilly Steamship Company (ISSC) which operates Skybus flights year-round to St Mary's.
After the withdrawal of the helicopter service from Penzance, Skybus has become the last link from Cornwall to the Isles of Scilly.
Plane flights by Skybus operate from Bristol, Exeter, Land's End, Newquay and Southampton, but are more susceptible to bad weather than the helicopters.
BBC: British International Helicopter on Tresco. Pic: D Sims
Skybus engineering manager Mick Yould, who has spent three weeks in Canada preparing the plane, said it was "a really tough piece of kit".
"Every booking counts, so although I think Skybus has been doing a pretty good job since the helicopters stopped, it's quite worrying, " he told BBC News.
Skybus has transferred all flights to Newquay until 6 December.
Air Southwest has said it will try to reschedule flights to fly from Plymouth airport, while Skybus, which flies to the Isles of Scilly, will use a facility at Lands End.
The Isles of Scilly Steamship Group, which owns and operates Skybus, said having a fourth Twin Otter would give it more flexibility on its routes from Exeter, Newquay and Land's End.
"It's a great aircraft for us because of its short take off and landing capability, but they are not easy to get hold of because they are so popular, which is why we had to go to Canada, " Skybus chief executive Jeff Marston said.
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