Swiss challenger Alinghi came from behind to narrowly beat defending champions Team New Zealand in the America's Cup on Sunday.

The win put them 2-0 ahead in the best-of-nine race for sport's oldest trophy.

Team New Zealand, already reeling from a disastrous first-day loss Saturday during which their radical new boat almost sank, led for most of Sunday's race.

But Alinghi surged ahead on the sixth and final leg to finish seven seconds ahead.

The team, the people, always make the difference and we have a strong team Alinghi's Jochen Schuemann

Team NZ skipper Dean Barker and his crew looked to have put Saturday's disappointment behind them when they sailed past Alinghi on the second leg of the race.

The black New Zealand boat later opened up a lead of almost 200m but Alinghi, with former Team NZ skipper Russell Coutts at the helm, fought back aggressively.

The lead changed three times on the final leg as Alinghi regained and then surrendered the lead.

But biotechnology heir Ernesto Bertarelli's team snatched the lead back again within sight of the finish line and kept Team New Zealand at bay in a tense run to the finish.

"The afterguard did a nice job of playing the shifts down the first run and we took advantage of a bit of a separation," said Barker.

"But on the last run we made a couple of mistakes early on and that caused the race to end up being a lot closer than it needed to be.

"They went outside us just at the end."

Alinghi's Jochen Schuemann insisted his team's better crew work was the difference.

Barker's team have a mountain to climb

"The team, the people, always make the difference and we have a strong team," he said.

"We went through tough competition in the Louis Vuitton already, and all the preparation, with our shore team and sailmakers, all the effort of the past three years is now paying off."

The start of the second race was delayed for more than two hours by light winds and hundreds of spectator craft which drifted on to the course.

Team NZ's troubled America's Cup campaign slipped further into crisis on Sunday when they revealed their backup boat, NZL-81, suffered "serious structural problems" before Saturday's first race.

The problems with NZL-81 compounded difficulties suffered aboard its sister, NZL-82, which broke and almost sank on Saturday, then lost Sunday's race by seven seconds.

Team NZ refused to go into details about the damage NZL-81 suffered while trialing with NZL-82 in strong winds and choppy seas before the opening race.

The third Cup race will be sailed on Tuesday after a scheduled off day on Monday.