Ministers have made literacy and numeracy targets, measured by the tests, the centrepiece of their policy for raising standards.
But in remarks revealed today, Mr Woodhead argues that the tests are vague, unreliable and "administered creatively" by schools - a reference to allegations of cheating.
National tests that must be taken by all pupils at the ages of 7, 11 and 14 are used by the Government as a yardstick to judge schools. League tables for primary schools, to be published in February, are based on test results for 11-year-olds.
But a report in today's Times Educational Supplement discloses that Mr Woodhead told a seminar at the London School of Economics last week: "There are no reliable national curriculum tests.
"I have not got a lot of faith in them for three reasons. First, I am not sure the tests are the right tests. The concept of levels [broad measurements of pupils' achievement] is a very vague one. We need standardised tests in literacy and numeracy.
"Second the tests have changed quite significantly over recent years, so it is impossible to compare like with like. Third, a lot of individual tests are being administered in a creative way."
The Qualifications and Curriculum Authority, which administers the tests, introduced new security measures this year after complaints about cheating last year. There were allegations that teachers opened test papers in advance and coached children, and that some pupils were given extra time.
This year, officials carried out spot-checks in 2,000 schools just before the tests in May but found only one case worth investigating.
Yesterday, the authority and the Government reaffirmed their faith in the tests. A statement from the authority said: "Successive governments have used the national tests as the most reliable way of measuring children's progress. The tests cannot be bettered as a way of giving teachers and parents information on progress."
A government source said: "We have strengthened the maths test this year by introducing a mental arithmetic test for the first time and we have also tightened up on security. National tests are the basis on which we are determined to make progress towards national targets."
David Hart, general secretary of the National Association of Head Teachers, said: "For the Chief Inspector of Schools to cast doubt on the tests' validity and to imply that schools are cheating, seems to potentially undermine a central plank of the Government's standards agenda."
Peter Smith, general secretary of the Association of Teachers and Lecturers, said: "It has taken a long time for Chris Woodhead to catch up with what teachers are saying about these tests. Does he accept that his inspectors should treat the results with great caution?"
A spokesman for Mr Woodhead's Office for Standards in Education said he had been speaking at a private seminar for academics about the reliability of data.