Election campaigning in Cardiff, Michael Fallon said such a government would mean "chaos and instability".
Hearing the Welsh Tory leader had not read his party's UK manifesto, Mr Fallon said it was "well worth a read".
Labour said the Conservatives had not ruled out a "dangerous pact with UKIP".
Mr Fallon told BBC Wales said there was a "threat of instability, of putting our economic recovery at risk, if you end up with a minority government".
"It's becoming clear that Labour can't form a government on their own and a cobbled together coalition or minority government, depending day after day on the support of other parties, is simply a recipe for chaos and instability.
"The only way to have a sure, certain government that would continue the recovery and the 50,000 new jobs in Wales is to vote Conservative."
Responding, a Welsh Labour spokesman said: "The Tories have consistently not ruled out a dangerous pact with UKIP, that would risk the tens of thousands of jobs dependent on Britain's place at the heart of the EU."
The spokesman added: "The IFS [Institute for Fiscal Studies] lifted the lid on the Tories extreme spending plans today, which would be disastrous for Wales."
Liberal Democrat candidate Roger Williams said no party would win a majority and an "unstable government....pulled sharply to left or right" would "cost us all dear".
"This is why we need the Liberal Democrats in government, providing a stable government that can build both a stronger economy and a fairer society."
The Conservative defence secretary has warned a Labour minority UK government, or "cobbled together" coalition involving Plaid Cymru and the SNP, would put economic recovery at risk.