The ex-St Kilda mentor aired his concerns in the wake of coach Scott Watters' sacking on Friday.
"Our next bastion to me seems as though it might be New Zealand and that to me means that St Kilda could potentially be lost to Melbourne and the AFL," Thomas told AFL.com.au.
"I think St Kilda should be competing as a top-four or five Melbourne-based AFL club rather than dithering around at the other end and having the same trials and tribulations (as others)," he said.
Thomas gave no indication he was against the AFL's New Zealand push, but doesn't want see the Saints form part of it.
"I'd like to see St Kilda back out of the New Zealand deal firstly, and secondly if the AFL's serious about its global expansion New Zealand is the obvious next port, and quite clearly the AFL is investing a lot of money to ensure that that happens," Thomas said.
"I can't understand how in five to six years' time, nearing 2020, how they're going to be able to unravel the St Kilda footy club out of that and put a new club in or start a new club," he said.
"To me it just seems like if you're going to be playing one, two and eventually three or five games a year in Wellington and maybe some in Auckland as well, I suppose in eight to 10 years, it makes sense that St Kilda is the choice to do that."
The Saints played the Sydney Swans in Wellington on Anzac Day this year, and will play Brisbane Lions there in 2014.
The agreement with officials in Wellington allows for additional fixtures in the future.
When the New Zealand deal was first announced in September last year AFL deputy CEO Gillon McLachlan didn't rule out having a permanent team across the Tasman one day.
"Where that goes, I don't know. Whether it's a team in 10 years, I'd love to think it was," McLachlan said at the time.
St Kilda immediately touted its recruitment of Kiwi-born Shane Savage from Hawthorn as a boon for the relationship with New Zealand.
Twitter: @MattThompsonAFL
