Police said offenders broke into the store in Station Street just over a week ago and stole $10,000 worth of the popular toy.
The burglars then fled the scene in an unidentified vehicle.
They returned sometime between Sunday afternoon and Monday morning and stole items totalling $5,000, including Lego "City" and Lego "Technic", police said.
Detective Senior Constable Ian Porter said he believed the robbers had some kind of glazing experience and that there were multiple people involved.
"They've removed the entire glass panel from a front automatic sliding door," Detective Senior Constable Porter said.
The thieves also appeared to have been planning a second robbery, as they took the store's CCTV hard drive during the first heist, he said.
"On the second occasion the store manager hasn't been able to replace the CCTV in time, so they knew what they were doing," he said.
"We believe it's an organised group of people who've done a bit of planning and homework."
Werner Baumann said he had never experienced a robbery like this in 15 years of managing the store.
He said the thieves stole about 60 to 70 per cent of his stock before they returned.
"They've come back and taken just about all the rest of the Lego that we had in our stock," Mr Baumann said.
Mr Baumann said he does not believe the theft was an isolated incident.
"It's fairly far and wide, as the police have been finding out, it goes from NSW right down into Melbourne," he said.
"A group of people have been targeting toy shops and primarily just stealing the Lego."
He said he will not be able to replace some of the stolen Lego.
"We had stock on our shelves that could have been one or two years old that you can't reorder again through Lego, so it would be sought after in the right hands," he said.
Detective Senior Constable Porter said he believed the Lego was destined for resale and urged vigilance in dealing with second-hand sellers and online trading sites.
"We'd just like anyone... to keep a lookout at stalls, markets and on Gumtree or eBay," he said.
"It's a popular brand and many people buy them for their children or for themselves."
Detectives also appealed to anyone who may have witnessed the incident or seen suspicious activity in the area to contact them.