A spokeswoman for Lotto NZ said shutting the site down at 7.30pm - just before the 8pm Lotto draw on Saturday night meant there were fewer tickets "in flight" being purchased or checked.
Lotto NZ corporate communications head Lucy Fullarton said shutting the site after ticket sales closed on Saturday rather than Wednesday meant an extra day to purchase tickets once the site had opened again.
"It probably does seem counterintuitive, but the best time to upgrade our systems is after the draw has closed and we've completed the post-draw activities, but before players have bought tickets to the next draw," she said.
"It allows us to conduct the draw, complete all the ticket processing, and means tickets are not 'in flight' (ie being bought or checked) as we're trying to move to a new system."
Fullarton said it also gave more time to make sure everything was working well before the next Lotto draw.
And despite frustrated players describing Saturday as Lotto's biggest draw, ticket sales were driven more by the size of the jackpot.
Lotto is drawn only on Saturday and Wednesday nights. One of the biggest Lotto wins - a $42.2 million prize - was from the Wednesday night draw.
Last night's jackpot was $10 million and was not struck.
The upgraded site went live on Sunday morning but there were issues.
"Following the upgrade last night, we opened the site this morning, and players can log in, check account balances and play games," Fullarton said.
"However, we are seeing an unanticipated technical issue which means players are not yet able to view or check tickets – or are only able to do so intermittently."
Fullarton said the issue was Lotto's "top priority" and the team was working hard to resolve the issue.
Lotto NZ had warned players earlier in the week of the system upgrade.
Players were told the planned maintenance on Lotto's app and website meant they wouldn't be able to check instantly if they were a big – or small – winner.
The maintenance was expected to continue to an "unspecified time" on Sunday.
The numbers in last night's draw were 31, 3, 18, 34, 16, and 30. The Powerball was 8 and the Bonus Ball 17. The Strike numbers were 31, 3, 18 and 34.
Powerball was not struck so will roll over to Wednesday night, where the jackpot will be $12 million.
First Division was struck, with three lucky Lotto players each winning $333,333. The winning tickets were all sold on MyLotto to players from Auckland, Nelson and Canterbury.
Strike has also rolled over and will be $300,000 on Wednesday night.