Labor's Kristy McBain has claimed victory after Saturday's by-election in the federal NSW seat, and at 4pm on Tuesday led Liberal rival Fiona Kotvojs by 731 votes as counting continues.

Mr Barilaro, who publicly toyed with the idea of running as the Nationals candidate in the seat that overlaps his state electorate, has come under fire from coalition colleagues as Eden-Monaro slips from their grasp.

But the NSW Nationals leader argues his personal brand helped, not hindered the coalition's chances of claiming a once-in-100-year by-election win.

"There's no blame to take because if you want to go down that path ... they attribute the success of Queanbeyan to me," he told reporters in Sydney.

"That's my seat. That's my area. That's the area that I've worked hard."

The state deputy premier shot down suggestions that he sabotaged Dr Kotvojs by telling Nationals supporters to preference Ms McBain ahead of her.

"There's been a lot of speculation by, unfortunately, the Liberal Party," he said.

"It's easy to blame people, but I know our how-to-vote card - I was on radio on Friday backing in a one-two National coalition.

"I was there on election day backing in the coalition."

Mr Barilaro instead pointed the blame at the Shooters, Fishers and Farmers Party which backed Labor in a betrayal of the party's conservative roots.

"There were 14 candidates in the field - 12 of those candidates preferenced the Labor Party," he said.

"It's the Shooters that actually won Labor the election."

The NSW Nationals MP, who hasn't closed the door on contesting the bellwether seat at the next federal election, said Ms McBain, the former Bega Valley Shire mayor, would be a "fantastic asset to parliament".

"I know that the people of Eden-Monaro have actually elected a very good local member, regardless of what political party they are (from)," Mr Barilaro said.

Australian Associated Press