Alderney Renewable Energy said there would be "no impact on war graves".
Image caption Bore holes have been dug at Longis Common, a sensitive historic area.
Four labour camps were built in Alderney during the Nazi occupation of the Channel Islands.
Some historians put the number of deaths among workers and slave labourers - many of whom were Jewish or Russian - above 1,000.
JTrails believes graves of prisoners may be at Longis Common - one area where drilling was carried out in preparation for the FAB Link, which is due to be completed by 2020 at an estimated cost of Â£500m.
Marcus Roberts, JTrails director, said: "It is a matter of great concern if a war grave site is being potentially disturbed."
Mr Roberts said he believed more Jews died at Longis than at any other part of the island.
He added: "We are not against development, but it shouldn't be disturbing [potential war graves]."
The developer said it had undertaken a non-intrusive geophysical survey to "detect any areas of unknown archaeology" in the area.
Executive director Declan Gaudion said: "The proposed route for crossing Alderney has been very carefully selected with full support from the States and the Alderney Society."
Alderney politician Graham McKinley said there was "some concern and differences of opinion" on the island.
He added: "We are concerned about the possible discovery of human remains. We have to be very careful."
Occupation of the Channel Islands
- The islands were the only British soil to be occupied during the war
- After the German offensive raced through France, the British government decided the islands were not strategically important and left them undefended
- This was not communicated to the Germans, who bombed Guernsey's St Peter Port Harbour and targets in Jersey, killing 44 people
- German troops landed in Guernsey by plane on 30 June 1940 - the start of five years of occupation
- The islands were turned into an "impregnable fortress" on the express orders of Adolf Hitler
- Four labour camps were constructed in Alderney
- A fifth of all the defence works in the Atlantic Wall - a defensive line stretching from the Baltic to the Spanish Frontier - were built on the islands
- The islands' governments continued under German rule, which some saw as collaboration