"I believe in this great country of ours, and I believe in one nation, undivided, called Canada," Chong, whose cabinet brief included Ottawa's ties with the Canadian provinces including Quebec, told a news conference.
"They [the separatists] will argue that if the Quebecois are a nation within Canada, then they are certainly a nation without Canada."
Chong's resignation does not threaten the survival of the conservative government, but highlights political tensions over the status of Quebec, which has previously held two failed referendums on independence.
The parliamentary motion was drafted last week by Stephen Harper, the prime minister, in response to one from the Bloc that recognised Quebecers as a nation, but did not include the words "within a united Canada".
The news for Harper did not improve later on Monday when Conservative candidates did poorly in two by-elections to fill vacant seats in parliament.
As expected, the bloc easily retained control over its stronghold of Repentigny in Quebec, winning 67 per cent of the vote compared with just 19 per cent for the Conservatives.
Chong said he remained a Conservative member of parliament and was loyal to Harper.
He resigned after the government said it would dismiss cabinet ministers if they did not vote for the proposal.
Quebec already calls its legislature the Quebec National Assembly and calls Quebec City its national capital.