The plane was on its way from Norwegian airport Gardermoen to Tromsø when it sent out a distress signal in Swedish airspace at 11.31pm on Thursday night.
West Atlantic -- the plane's operator -- did not immediately identify the crew but said that the captain was aged 42 and from Spain, and the first officer was aged 34 and from France. Between them they had logged more than 6,000 flight hours.
On Friday morning the CEO of the company told a press conference in Gothenburg he had "great sorrow" that the accident had taken place.
"What should not happen and may not happen has happened," Gustaf Thureborn said to reporters.
A plane similar to the one that crashed, pictured in 2010. Photo: Tom Gulbrandsen/TT
Police and mountain rescue teams arrived at the site at around 1pm on Friday, after being delayed by treacherous conditions.
However Swedish emergency services reported later on Friday afternoon that it was likely the pilots had died in the crash and said that staff were no longer looking for survivors.
The cause of the crash remains a mystery, officials said.
A Norwegian F16 plane first located the wreckage on the ground between the north-western edge of Swedish lake Akkajaure and the Norwegian border, in an area often known as the Swedish alps.
Thureborn told reporters he was woken up by a phone call two minutes after the airline was alerted about the crash and was at the office 15 minutes later.
The aircraft, a Bombardier CRJ-200, is registered in Sweden, but travels between Norwegian destinations. It was manufactured in 1993.
Thureborn told reporters that all of the company's planes of the same model had been grounded as a precaution.
"In light of the ongoing investigation we can't give you more information about what has happened, but we'll have to await its results. We're happy to offer more information as soon as we have it," he added.