The tests have been made tougher and Mrs Morgan says lower results should not be interpreted as a decline in performance by pupils.
"They simply cannot be compared directly," says Mrs Morgan.
Heads have called for this year's test results not to be published.
Mrs Morgan's warning comes in advance of the publication of results from Sats tests taken by 11-year-olds, which this year have been made more difficult and based on a new curriculum.
There will be national level results published on Tuesday and individual schools will receive their results.
There has been an expectation of volatile and unpredictable results - and Mrs Morgan is pre-empting claims that they will show that standards are falling.
"I expect critics of the new primary curriculum will be quick to try and suggest that any lower results are evidence of a failure of the system," says Mrs Morgan.
"Nothing could be further from the truth. I don't know what the results will look like yet. But I have always been clear that politicians trumpeting ever-rising test results, at the expense of high standards is entirely wrong."
If results do turn out to be lower than previous years, then Mrs Morgan feels: "It wouldn't mean children have performed any worse this year; simply that we have raised the bar on what counts as good enough.
"Neither schools nor parents should try to compare this year's results with previous years. The tests are new and are based on a new, more rigorous national curriculum - based on the best evidence from across the world."
Mrs Morgan said that parents should "see the results as what they are - a reflection of how well children this year have performed against a new curriculum".
The National Association of Head Teachers had previously written to the education secretary calling for the publication of this year's results to be cancelled.
They warned that there had been "serious mistakes" in how changes had been introduced and said results were too "unpredictable" to be used for league tables.
Head teachers said the results were likely to be so "skewed" that "comparisons between schools become very risky".
Kevin Courtney, acting general secretary of the National Union of Teachers, said the results would be used by the Department for Education and Ofsted to make judgements on schools, with potentially "serious consequences for the jobs of school leaders and the future of the school".
But he said that from the perspective of teachers, the changes to the tests had been "shambolic", with frequently changing guidance and leaked test papers.
The results of Sats tests taken in primary schools in England, due to be published on Tuesday, should not be compared with previous years, says Education Secretary Nicky Morgan.