Trees for Life said a mother and at least two kits have been observed on a river near Beauly.
It has asked that the mammals be allowed to remain where they are or be relocated.
The government has instructed that the beavers be trapped and then kept in captivity.
Trees for Life believes the animals have been in the area for at least five years.
The presence of beavers has been found previously in the Highlands.
In 2008, one was found dead on a beach at Eathie on the Black Isle after suffering what police described as a "cruel" death after ingesting a large quantity of sea water.
Police suspected the animal was linked to illegal releases of beavers in other parts of Scotland.
Native Scottish beavers were hunted to extinction in the 16th century.
Last year, the Scottish government announced that beavers reintroduced to Scotland could remain and were given protected status.
Eurasian beavers taken from Norway were released at Knapdale in Argyll in 2009. An illegally-released population has also been discovered in Tayside.
Both groups will be allowed to expand naturally but will be managed to protect farmers and land owners.
But in the case of the Beauly beavers, Environment Secretary Roseanna Cunningham said the animals had been released illegally and must be removed.
She said: "We have been clear that we are minded that beavers can remain in Scotland and that their range can expand naturally.
"But the unauthorised release of beavers is a criminal offence and will damage the beaver reintroduction project.
"That is why I am asking Scottish Natural Heritage to take swift action in the Beauly area. We must avoid a repeat of the experience on Tayside."
Alan McDonnell, conservation projects manager at Trees for Life, said the government's decision was "disappointing".
He said: "Whilst we understand that the minister wants to address the concerns of landowners in Tayside, the situation here is very different and we think it is possible to consult and negotiate with landowners in the immediate vicinity of the family and upstream to find an alternative outcome for the animals.
"We think these beavers have been active at this site for at least five years without any local concerns being raised. Which just goes to show that in the right location, beavers and other land use interests can co-exist successfully."

SKN Heritage Museum is showing the type of belongings brought by African-Caribbean immigrants in the 1940s and 50s.
The Windrush generation responded to adverts to work in Britain but were only allowed to bring one suitcase.
Organisers said the display gives a unique insight into important part of Nottingham's history.
The Windrush was named after the first boat which brought people from the Caribbean to Britain in 1948.
The exhibition, called 'From Caribbean Isles to the British Isles -Home to Home', aims to give an insight into people who travelled across the Atlantic to seek a better life in what was still the Empire's "mother country".
Item include photographs, clothes, records and games - as well as beauty products designed for black skin and hair when none were commercially available.
Catherine Ross, the museum's founder, cameto Nottingham from St Kitts when she was just seven years old.
She said: "Our aim is to let everyone know about the contributions that Caribbeans have made to British society and Nottingham and commemorate these achievements.
"There'sno better place tostart than Nottingham Carnival, as it's such awell known and celebratory event in Nottingham's calendar."
The carnival is taking place for the first time take in two sites - the Forest Recreation Ground on Saturday and the Victoria Embankment on Sunday.
A conservation charity has asked the Scottish government to protect a family of beavers found to have been released illegally in a part of the Highlands.
[NEXT_CONCEPT]
A unique perspective on a landmark social event is to be unveiled as part of Nottingham's Caribbean Carnival.