Of the 7053 votes counted from booths in the Snowy Valleys as of Monday morning, more than 39.5 per cent of primary votes went to Dr Kotvojs.

Ms McBain secured just over 32.1 per cent of primary votes in the Snowy Valleys but was headed to victory with 50.4 per cent two-party preferred vote across Eden-Monaro.

Charles Sturt University associate professor in political science Dominic O'Sullivan said people should take caution when interpreting the results but it did appear that Prime Minister Scott Morrison's national popularity had not made much of a difference.

"Overall the swing against Labor on primary vote was three per cent and a good deal of that or possibly all of it could be explained by [departing Eden-Monaro MP] Mike Kelly's personal standing," he said.

The Shooters, Farmers and Fishers Party candidate Matthew Stadtmiller scored more than double his Eden-Monaro average in Snowy Valleys with 10.8 per cent.

Dr O'Sullivan said the National Party candidate Trevor Hicks seemed to have suffered a "protest vote" in the Snowy Valleys, with the party's primary vote down by nearly 1.2 per cent compared to the whole electorate.

"[The Shooters] do tend to pick up a protest vote, especially from the Nationals," he said.

The busiest Snowy Valleys voting location, the Tumut Pre-Poll centre, recorded nearly 41 per cent of its primary votes for Dr Kotvojs, who also had the highest vote count at all the council area's booths except Tumut East.

The figures did not include any postal ballots that were mailed by voters living in the Snowy Valleys.

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When asked about the results in Snowy Valleys, Ms McBain said she would work for all people in Eden-Monaro.

"I'm looking forward to getting down to work - and working with all levels of government to get the best outcomes for the people of Eden-Monaro, especially for the Tumut, Adelong, Tumba and Batlow communities," she said.

"I'm looking forward to working for all members of the community across this vast electorate - no matter who they voted for.

"A key priority will be to fight for greater support for our forestry sector, orchardists and farmers on the South West slopes, particularly after bushfires and drought."

Dr Kotvojs has yet to concede defeat but told the ABC on Monday "with most of the votes now counted, we're very confident that Labor will retain the seat".