The proposal is contained in documents obtained by The Canadian Press under freedom of information laws.
Fisheries Minister Keith Colwell confirmed Wednesday that the province's newly elected Liberal government is reviewing the idea.
However, he said building a new, bio-secure lab would be the most expensive option among three proposals aimed at increasing monitoring of the aquaculture industry.
"If we decide to go with a new building it'll be down the road a little bit," he said. "We've got to review that. We're taking things slowly and making sure we get the best impact for the dollars we invest."
The proposal was first floated internally last year when the former NDP government was in the process of relocating 34 Fisheries and Aquaculture staff in Halifax to more rural locations, including Shelburne.
"We're going to look at construction of a new building again, but the other options on the table are far less expensive," Colwell said in an interview.
He said the province has the option of sticking with the status quo, which means most of the lab work needed to monitor Nova Scotia's aquaculture sites would continue to be handled at government facilities in Truro.
"If it works very well, we'll maintain what we have," the minister said.
The third option on the table is building or leasing a facility in Shelburne that would include a sample preparation room, which would transfer its samples to Truro and elsewhere for analysis.
The documents say that even though building a new lab in Shelburne would be expensive, such a facility would better serve the growing aquaculture industry.
"(Having) fish veterinarian capacity in Southwest Nova and in Truro (would) provide provincial coverage," says a discussion paper prepared in November 2012.
As well, samples taken from sites in the region would be less likely to be "compromised" if they could be taken to a local lab rather than shipped to Truro or outside the province to the Research Productivity Council in New Brunswick and the Atlantic Veterinary College in P.E.I.
The proposed lab in Shelburne would be rated as a Level-2 site, which means it would be better equipped to contain infectious diseases, such as infectious salmon anemia, the documents say.
The lab in Truro is a less-secure Level-1 facility.
"Today's standard for fish health labs is Level 2," the documents say. "This increased standard reflects the increased level of risk related to the spread of infectious diseases within fish populations."
A new lab would also help the province better cope with its updated aquaculture program that requires an increased number of inspections, the documents say.
But the discussion paper offers a blunt assessment of the cost of such a facility.
"(The) high-cost option will attract negative attention," it says.
Colwell said the $2-million plan to relocate Fisheries and Aquaculture staff — part of a larger relocation program introduced by the NDP — has yet to be completed but appears to be within its original budget.
He said of the 34 staff asked to relocate, only four actually moved — two to Cornwallis and two to Shelburne. So far, all but five of the positions have been filled at the two locations, with most of the new workers coming from nearby communities.
"I'm very pleased with the staff so far, the ones that have moved and the ones that have taken up new positions," Colwell said.
In Opposition, the Liberals supported decentralization, but Colwell said it was done in too much haste.
"We're going to be reviewing it all, but we have no intentions of making any sudden moves."