That policy is also proving unpopular with resident crofters who say it is the wrong approach.
BBC: Possible European court challenge on crofting evictions
Paul Wheelhouse said lawyers were examining the possibility of letting the rights directly to the crofters.
Crofters on Skye and in Wester Ross have claimed the birds feed on their stock.
The scheme was run following crofters' claims that sea eagles were preying on the young animals.
The opening ceremony was staged amid a row between the club and seven crofters.
Scottish Labour leader Johann Lamont said a longer term commitment should be made to the crofters.
BBC: Raasay shooting and fishing rights returned to crofters
Anne Gillies, of the Raasay Crofters Association, said she was delighted by the move.
BBC: Raasay shooting and fishing rights returned to crofters
The firm out-bid Raasay Crofters' Association, which had managed the rights for 18 years.
BBC: Skye ministers back Raasay crofters in sporting rights row
Crofters on Scotland's west coast have complained in recent years about sea eagles taking young lambs.
BBC: Beaver killing may be necessary in future, SNH report says
He said the map-based register would be "costly and burdensome and add no benefit to crofters".
One of those concerned about the way in which absentee crofters are being challenged is Hugh Maclellan.
BBC: Possible European court challenge on crofting evictions
The crofters were opposed to an extension of the course onto land they used for grazing livestock.
The most vocal opponents of the Askernish project have been Gilbert Walker and William Macdonald, both crofters.
Raasay Crofters' Association, which made a lower offer for the lease, had managed the rights for 18 years.
Environment Minister Paul Wheelhouse said the crofters' association bid for the lease was "substantially" lower than the winning bid.
Mr Lomas' Pairc Crofters Ltd and one of its tenants, Pairc Renewables, appealed against the decision at Stornoway Sheriff Court.
He said tackling absentee crofters and neglect of crofting townships would also lead to homes becoming available to new inhabitants.
Not bad for a drink that was invented by poor Scots crofters trying to keep out the chill of a Highland winter.
Dr Jessie Lovie Watt , lately Crofters' commissioner (Insch, Aberdeenshire) - For services to Crofting and to Agriculture in Shetland and Orkney.
Conservative MSP John Scott said it was in the interest of farmers, crofters and the Scottish government to find a different system.
Earlier, Environment Minister Paul Wheelhouse told BBC Scotland the crofters' association bid for the lease was "substantially" lower than the successful bid.
BBC: Skye ministers back Raasay crofters in sporting rights row
He told BBC Radio Scotland's Out of Doors programme the impression had been given that the crofters had been given a "rough deal".
But after a row, the firm and the government came to an agreement that allowed Raasay Crofters' Association to hold onto the lease.
Environment Minister Paul Wheelhouse said Raasay Crofters' Association has been given the lease until 1 March to allow time for the consultation to happen.
Following a public and political row, South Ayrshire Stalking gave up its claim to the lease and Raasay Crofters' Association was awarded an extension.
Ms Boyack said the new register would impose financial burdens on crofters which they could ill afford and it could be divisive and bureaucratic.
Absentee crofters being evicted for not using their land have joined forces to challenge the decision and may take their fight to the European courts.
BBC: Possible European court challenge on crofting evictions
The lease to manage shooting and fishing rights on Raasay could remain in the hands of crofters long term, the environment minister said last week.
It added that it tried very hard to work with crofters.
BBC: Possible European court challenge on crofting evictions
They're all on all utility services, like water and electricity, but they've been left to rot, because crofters couldn't pay the VAT to do them up.
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