Thousands of farmers across Scotland were left out of pocket to the tune of hundreds of millions of pounds thanks to the IT blunder, with a third still waiting for payments they were told to expect in December.
The commitment will be among a series of measures unveiled at tomorrow's launch of the 'Standing up for Rural Scotland' document, which will form part of the party's wider Holyrood manifesto.
Any inquiry would not only uncover what went wrong, but also ensure mistakes aren't repeated, and that by the time next year's payments are due, there is a guarantee the system will be working efficiently.
The document will "demand an independent inquiry into the farm payment debacle to ensure that in future Scottish farmers are not left wondering when, or even if, vital payments will reach them".
It adds: "In the next parliament we will make sure that in future, when the option for making early payments is made available from the European Commission, that option is taken up."
The Scottish Government was forced to set aside an emergency fund of £200 million after the IT system designed to process payments failed, despite running heavily over-budget.
It prompted farming leaders to call for the resignation of rural affairs secretary Richard Lochhead and gather in protest outside the Scottish Parliament earlier this month.
Scottish Conservative leader Ruth Davidson said:
"Farming is at the heart of Scotland's rural economy.
"Our producers deserve better than SNP mismanagement.
"That's why it's essential the SNP's CAP payments fiasco is properly investigated.
"This is not just a case of finger pointing - it's about looking ahead to ensure these mistakes are not repeated.
"We need to identify what went wrong, fix the system and make sure it works in the future.
"Farmers need to plan ahead, but they can't do that properly if they have no idea when - or how much - money is coming in.
"If the CAP payment fiasco had affected the central belt or urban Scotland, the SNP would have been quick to act. But because it was rural Scotland, they ignored the warnings and dragged their feet.
"The priority now is to make sure the CAP payments system works, which is why this inquiry is so important."