Ben Hyne went down with serious knee injury in the 78th-minute and despite play coming within five metres of the ACT Brumbies flanker, there was no stoppage.

The referee stopped play after the Eagles had marched 25 metes down field and earned a penalty, but have used their entire bench the Vikings were unable to replace Hyne.

NSW punched the corner and scored the match-winning try as the Vikings conceded 10 points in the final five minutes to lose 25-24 in Armidale.

The decision to continue play around Hyne led to a heated exchange between the Vikings medical staff and the referee, while Sampson called for better player welfare.

"Yeah that was really disappointing, it's a serious injury and I think it could have been managed a bit better," Sampson said.

"They've been strict on it all year and our medical staff wanted to get out to him and stop the play but it wasn't to be. We'll review the tape and communicate any concerns during the week."

It wasn't the only decision which irked Sampson after an Eagles' maul on the final play lineout collapsed but play was allowed to continue.

"The communication we got was that it was a maul and the maul collapsed and there was a good two to three seconds with it stationary on ground," Sampson said.

"I've seen a lot of calls go the way of defending teams there and we were surprised it didn't go our way, but we'll stay positive and keep doing that maul defence and get that call next week."

Vikings hooker Folau Faingaa scored two first-half tries against his former team as the Vikings held a 14-10 lead at the break.

Canberra barely touched the ball in the first 18 minutes of the second half, before Andrew Robinson scored an intercept try against the run of play and extended the lead to 21-10.

Vikings flyhalf Wharenui Hawera looked to ice the game with a 73rd-minute penalty for a 24-15 lead, but the Eagles rallied late to win off the boot of Tayler Adams.

The Eagles flyhalf nailed a 43m penalty with four minutes remaining and then slotted a sideline conversion with the final play of the game to hand Country their first win of the season.

It marks two close losses in a row for the Vikings but Sampson said there were still plenty of positives heading into their clash against Fiji Drua at Viking Park on Friday.

"I was very happy with our defence and I thought at the end of the game we should have been rewarded for that but wasn't to be," Sampson said.

"Tommy Cusack was good in tight and Ben Hyne had a big game before he got injured and if it's serious he's a huge loss, he's got a big engine and has provided a lot in attack and defence."