Prolonged wet spring conditions were likely to increase rabbit numbers dramatically, he said.
The ACT in 2010 reported its wettest year in a decade, following a long-running drought.
Mr Stanhope will raise the issue at a meeting of Australian agriculture ministers on Monday.
He also has written to federal Agriculture Minister Joe Ludwig and his NSW counterpart Steve Whan.
"If left unchecked a rabbit plague could have severe impacts for local farmers and the territory's native ecosystems," Mr Stanhope said in a statement.
The ACT government has committed $500,000 to fund to rabbit control up to 2012.
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