But medical checks and a full recovery has left him determined to play in the first Test against Ireland in Hamilton on Saturday.
He missed the All Blacks' Grand Slam tour of Britain last year due to an injury sustained late in the National Provincial Championship and when the heart problem occurred again it was feared he would miss the weekend's Test.
"I guess I was a bit scared, but I was in the best hands and Doc Deb [team doctor Deb Robinson] was with me the whole time so there was nothing to be worried about," McAlister said.
"She said it was nothing too major. The previous one I had for half an hour, just an irregular heart rate, this one the other day went for a bit longer.
"We had the right things to get it back to normal.
"When I first felt it, I thought it would go away but I went and saw Deb and we went to hospital. So, again, I was in the best hands.
"If it comes again we will deal with it the best way possible and I just not try to think about it really."
Robinson revealed it is unlikely that the problem would occur in a game as it appears to be triggered when McAlister was in a resting state.
"It has never happened during a game," she said. "He had the problem two years ago and he has played a lot of footy in the last two years and it has never happened in a game so that would be quite a long way down the list [of causes] really."
With first-choice fly-half Dan Carter selected for the Argentinian leg of the All Blacks' preparation, the series represents a great chance for McAlister to confirm his place as top understudy.
"It's going to be huge game, a good one for all of us and a good way to start off the season," McAlister said.
"They've changed a lot from the days when we used to give them a good, fair hiding. They're using the ball a lot better and are unpredictable as well.
"It's definitely going to be a tough game."
McAlister claims the All Blacks are committed to attack and, while not divulging the game plan, he said they would attack from most areas of the field.
But he is open about his own role.
"You have to have a bit of a mix, you can't just be a kicker and you can't just be a runner," he said. "You've got to have that rugby brain as well and know when to kick and when to run."