The World No 19 Ferns pulled one back through prolific striker Amber Hearn who headed home for her 53rd international goal for New Zealand, but the Kiwis could not find the late equaliser. After a NZ corner was cleared, substitute CJ Bott delivered a cross to the far post for Hearn to finish with a powerful downward header.
Football Ferns coach Tony Readings said he was happy with the performance in the team's first game in six months, but ultimately they were frustrated they didn't get anything from the game.
"We played well so it is one of those games you come away very disappointed to lose," said Readings. "We didn't start as well as we would have liked, but we came back into the game, and had the chances where we could have been up."
Readings said the team continued to create a number of chances in the second half but they could not finish and then were punished by Scotland.
"They have scored one completely out of the blue and we pushed forward and they scored again so they were two bitter blows but we kept going and we scored, and even after that second goal we had another couple of chances that we should have put away."
Football Ferns defender Ali Riley was also gutted with the loss, but felt the team will get better with more time together on this tour.
"We are always disappointed with a loss, but we are trying a new formation which created a lot of opportunities to get our fast players in behind. There were definitely some opportunities for us to build off but we were a bit disorganised with that new formation and they punished us when we were out of position."
The Ferns will look to bounce back in their second game of the Cyprus Cup against World No 24 Austria on Saturday (1.30am NZ time) at the same venue.